S.H.I.E.L.D.

"The principle S.H.I.E.L.D. was founded upon was pure [...] Protection. One word. Sometimes to protect one man against himself, other times to protect the planet against an alien invasion from another universe [...] but the belief that drives us all is the same, whether it’s one man, or all mankind." "That they’re worth saving."

- Nick Fury and Phil Coulson

The Strategic Homeland Intervention, Enforcement and Logistics Division, better known by its acronym S.H.I.E.L.D., is a United States extra-governmental military counter-terrorism and intelligence agency, tasked with maintaining global security. Founded in the wake of the Allied victory over the Axis powers and HYDRA in World War II, S.H.I.E.L.D. was organized to protect the United States, and later the entire world, from all possible threats. With its advanced weapons and extraordinary agents, S.H.I.E.L.D. was maybe the greatest military power on Earth. Run by Nick Fury and the World Security Council in the modern age, S.H.I.E.L.D. had to deal with the significant rise in enhanced individuals, dangerous advanced technology, and alien contact. But all the problems S.H.I.E.L.D. had to solve eventually led to the formation of the Avengers, a response team that was recruited to save the world during the alien invasion of Earth in 2012. The agency became publicly known after the Battle of New York, partially because of the Rising Tide website.

In 2014, through the actions of Captain America, the world became aware of the fact that S.H.I.E.L.D. was infiltrated and largely controlled by the terrorist organization HYDRA. After the battle in which S.H.I.E.L.D.'s primary headquarters, the Triskelion, was heavily damaged, all of S.H.I.E.L.D.'s classified files were dumped on the Internet, and the agency was disavowed by its commanding governments and labeled a terrorist organization. Many S.H.I.E.L.D. officials were taken into custody and subjected to rigorous questioning. However, despite the massive manhunt on S.H.I.E.L.D.'s agents, a few operatives scattered across the world in most secret bases remained loyal to their oath, saving the most necessary paraphernalia for future use. But the team most responsible for the survival of S.H.I.E.L.D. was the team of Agent Phil Coulson, who valiantly led his teammates against the forces of HYDRA led by the traitors John Garrett and Grant Ward, winning the battle in which Garrett's plan ultimately failed. After that battle, Nick Fury appointed Phil Coulson the new director of S.H.I.E.L.D. and tasked him with rebuilding the agency from scratch.

Now working from the shadows and hunted by almost every army in the world, Coulson used his old team as the core of S.H.I.E.L.D. and recruited mercenaries, former agents, and others to help fill the organization's ranks, while simultaneously continuing the fight against HYDRA. At the same time, another faction of S.H.I.E.L.D. arose, this one led by Robert Gonzales, who refused to accept Coulson's authority, believing his faction to be the only "real S.H.I.E.L.D.". After the Battle for the Kree City, Gonzales' faction revealed its existence, attacking and capturing Coulson's base, the Playground. This ignited an open conflict between the two S.H.I.E.L.D. factions. However, after successfully working together to attack and destroy the Arctic HYDRA Research Facility, Coulson successfully proposed a merge of the two factions which occurred in mid-2015. But the peace did not last long, as the Inhumans, a super powered humanoid race led by Jiaying, declared war on S.H.I.E.L.D. The fight was short and S.H.I.E.L.D. was able to prevent any further damage. After the war, Coulson started a new program of recruiting and training Inhumans for a team to deal with various threats.

The Inhuman Outbreak soon followed, and S.H.I.E.L.D. had to stand against the implications it caused. Following the exposure and the abrupt end of HYDRA's infiltration of the ATCU, S.H.I.E.L.D. was semi-legalized as the black ops division of President Ellis' administration, with the ATCU serving as S.H.I.E.L.D.'s public face. With HYDRA suffering a crippling blow, S.H.I.E.L.D. became aware about the dark Inhuman, Hive, and soon had to fight against his Inhuman army, which intended to transform all humanity into Inhumans. As the war with Hive reached its end, Agent Lincoln Campbell sacrificed his life to destroy Hive in a nuclear explosion in space.

In the aftermath of Hive's defeat, S.H.I.E.L.D. was once again legalized following the signing of the Sokovia Accords, but under a new Director, Jeffrey Mace. Daisy Johnson abandoned S.H.I.E.L.D. and became a vigilante known as Quake. At the same time they had to deal with a new threats, Eli Morrow, who with the knowledge of the mysterious book called the Darkhold, managed to gain incredible powers. In order to defeat him, S.H.I.E.L.D. worked together with Johnson and Ghost Rider. After the victory over Morrow, Johnson rejoined the organization. The revelation that Mace was not an Inhuman caused Coulson to return to the possession as the Director de facto. Following Holden Radcliffe's betrayal for the Watchdogs and the replacement of almost every key agent by an LMD by him, Agents Johnson and Jemma Simmons entered the Framework in order to rescue their missing friends. Despite the operation's success, they soon had to deal against Aida, who became an Inhuman seeking to destroy S.H.I.E.L.D. With the help of Ghost Rider they killed her, but it caused the organization's shutdown.

Foundation
"And S.H.I.E.L.D. was founded after the SSR was able to defeat the nearly indomitable force known as HYDRA."

- Leo Fitz

S.H.I.E.L.D. was formed shortly after World War II as a successor to the Strategic Scientific Reserve (SSR), an Allied deep science agency which fought against the Nazi sponsored special weapons division HYDRA during the war.

The founders of the new agency were Chester Phillips, the director of the SSR, Howard Stark, an industrialist of great wealth and a scientific genius, and Margaret "Peggy" Carter, the former partner of the American war hero Steve Rogers, better known as Captain America.

The agency's full name was the Strategic Homeland Intervention, Enforcement and Logistics Division, but some members of the agency preferred to call it by its acronym. The SSR was reformed as the scientific division of S.H.I.E.L.D. and continued to work on researching the advanced weapons captured from HYDRA as well as the mysterious Tesseract.

HYDRA's Rebirth
"After the war, S.H.I.E.L.D. was founded, and I was recruited. The new HYDRA grew, a beautiful parasite, inside S.H.I.E.L.D."

- Arnim Zola to Captain America and Black Widow

Shortly after the war, as part of Operation Paperclip, S.H.I.E.L.D. recruited the scientists of Nazi Germany as a think tank for the newborn agency. The infamous Arnim Zola was among the recruited scientists, but he used his new position to secretly rebuild HYDRA. With no one suspecting, HYDRA secretly grew within S.H.I.E.L.D., orchestrating many crises in the world over the next decades.

Cold War
S.H.I.E.L.D. was very active during the Cold War. In the 1980s, a group or radicals in the Soviet-controlled East Berlin obtained a piece of HYDRA technology and attempted to reverse-engineer it. The leaders of S.H.I.E.L.D. decided to send an agent to Germany and stop their plans.

However, a unique piece of equipment was needed for this mission: the Ant-Man Suit, which could shrink a human being to the size of an ant. The suit's inventor, Doctor Hank Pym, was unwilling to give it to anyone else, despite Howard Stark's demands, so Peggy Carter had to convince Pym to go on a mission personally.

Thanks to his suit, Pym was able to infiltrate the headquarters of the enemy group, discovering, they were actually a HYDRA cell continuing their old memory suppression experiments from World War II. Pym used his Ant-Man Suit to ruin the laboratory, free the prisoner and knock down all the guards. Later, he gave a report to Carter and Stark. In 1989, after his wife was apparently killed during a mission in 1987, Pym discovered that S.H.I.E.L.D. was trying to replicate the Pym Particles from the Ant-Man technology. He confronted Carter, Stark and Mitchell Carson at the Triskelion which was under construction. He pointed that this technology was dangerous and should not be used. He resigned before them from the organization and left the room furiously.

HYDRA's Moves
Over the years, one of the highest ranking S.H.I.E.L.D. members and the US Secretary of Defense Alexander Pierce was persuaded to join HYDRA. Later, he met Colonel Nick Fury, a distinguished officer of the United States Armed Forces and espionage veteran of the Cold War, and persuaded him to join the agency.

In 1989, Alexander Pierce granted Werner Reinhardt medical parole from his life sentence in the Rat and allowed the HYDRA general to return to Austria.

When Howard Stark became suspicious, he and his wife Maria were killed in an automobile "accident" secretly arranged by HYDRA on Long Island in 1991.

0-8-4
"We were headed into the Hunan province of China. A senior agent had called in an 0-8-4. An object of unknown origin. We've dealt with those before. He said the entire village had died trying to protect this one."

- Richard Lumley to Phil Coulson and Melinda May

In 1989, the entire population of a small village in Hunan Province, China, were killed defending a small infant. Designated as an 0-8-4 by S.H.I.E.L.D., a team was sent in to investigate. After losing contact with the main team, the back-end team, consisting of Richard Lumley, Linda Avery, and three other agents, investigated only to find the infant sleeping in the arms of the dead lead agent. The rest of the main team were dead. After returning to the United States, the other members of the team started to be eliminated. To ensure her safety, the infant was dropped off by Avery at the Saint Agnes Orphanage and arrangements were made for her to be moved to different foster homes to keep her safe.

Sarajevo
"I got fragged by an I.E.D. outside of Sarajevo. When I radioed for medevac, I got nothing but an earful of excuses. That's when I realized I was more loyal to S.H.I.E.L.D. than S.H.I.E.L.D. was to me."

- John Garrett to Grant Ward In 1990, Agent John Garrett was sent on a mission to Sarajevo,. During the mission, he was heavily wounded by an improvised exploding device. When he called for medical evacuation, his superiors replied that they could not send anyone. Angered, Garrett duct-taped his wounds, humped out of the city, and promised himself that he would repay S.H.I.E.L.D. one day for their treatment.

New Leadership
"What is all this?" "S.H.I.E.L.D. Strategic Homeland Intervention, Enforcement and Logistics Division. Your tax dollars at work. Hard work. We keep our fingers on America's pulse, and believe me, America has veins in every section of the world."

- Tony Stark and Phil Coulson

During a hostage situation in Bogota, Agent Nick Fury successfully saved all the hostages, including Alexander Pierce's daughter from rebels. Pierce was surprised by Fury's performance and later made him director of S.H.I.E.L.D.

Under Fury's leadership, the agency recruited some of the best marksmen and spies in the world, including Clint Barton and Natasha Romanoff. At that time, Agent Phil Coulson served as Fury's right hand man, though the actual deputy director of the agency was Maria Hill.

The Avengers Initiative
"There was an idea, Stark knows this. Called the Avengers Initiative. The idea was to bring together a group of remarkable people, see if they become something more. See if they can work together when we needed them to. To fight the battles that we never could."

- Nick Fury

During his directorship, Nick Fury had an idea to employ people with special powers and abilities to defend the Earth against threats that could be too complicated for S.H.I.E.L.D. to handle. He named that operation the Avengers Initiative.

Russian 0-8-4
"What was the mission you were on here?" "May and I were sent to retrieve an 0-8-4. Years and years ago."

- Daisy Johnson and Phil Coulson

Agents Phil Coulson and Melinda May were assigned to retrieve an 0-8-4 in Russia. As Coulson distracted the SVR agents, May retrieve the object. She then freed Coulson from the Russians and the two escaped with the 0-8-4.

The Legend of the Cavalry
"She took it upon herself to get them out. Said she could fix the problem. So she went in, crossed off the enemy force. Didn't say how."

- Phil Coulson to Skye

In 2008, S.H.I.E.L.D. took notice of Eva Belyakov's superpowered activities and tracked her down to Manama, Bahrain. A team led by Agents Phil Coulson and Melinda May was dispatched to analyze Belyakov for the Index. Belyakov assumed control of a group of gangsters and then held the entire S.H.I.E.L.D. team, minus Coulson and May, and a little girl, hostage within a warehouse. May ventured into the warehouse alone and crossed off the controlled gangsters and Belyakov. The little girl revealed herself as the controller of Belyakov, who was her mother, to May and nearly used her powers to kill the subjugated S.H.I.E.L.D. team, forcing May to kill her. For her role in saving them, the S.H.I.E.L.D. team gave May the nickname "The Cavalry", a moniker she grew to despise.

The story of "The Cavalry" became a legend at the S.H.I.E.L.D. Academy, with the story growing bigger and more inaccurate with each new class.

Kidnapping of Tony Stark
"I can be in Afghanistan by sunrise, Director Fury." "You can. But you won't. We're the Strategic Homeland Intervention, Enforcement and Logistics Division. Note the word "Homeland". We're not currently authorized for foreign ops."

- Phil Coulson and Nick Fury

A while later, wealthy industrialist Tony Stark was kidnapped in Afghanistan by the terrorist group called the Ten Rings. Since Stark was involved in making many weapons for the United States Armed Forces, Nick Fury sent Phil Coulson to Stark's business partner Obadiah Stane to investigate the possibility of Stark selling his country to save his own skin. Coulson returned with the negative reply, and offered to go searching for Stark himself, but Fury refused the offer. Three months later, Stark was found by the Army in the desert and brought back to the USA.

Birth of Iron Man
"I'm Agent Phil Coulson with the Strategic Homeland Intervention, Enforcement and Logistics Division." "That's quite a mouthful." "I know. We're working on it." "You know, we've been approached already by the DOD, the FBI, the CIA..." "We're a separate division with a more specific focus."

- Phil Coulson and Pepper Potts

Still suspicious of Stark, Fury sent Agent Coulson to talk with him, but without success. Shortly after, they discovered that Stark actually made an armored suit and used it not just to escape but also to repay to his kidnappers. A few days later, the agency's satellites detected an unmanned aerial vehicle flying through the streets of Los Angeles. It turned out the "vehicle" was actually Stark in the improved armored suit. Hacking of Stark's computers confirmed that Stark was working on the development of the armored suit.

A few days later, Fury and Coulson led a team of agents to the village of Gulmira in Afghanistan where they found an abandoned camera with the footage of Stark in another armor attacking the Ten Rings and destroying their piles of weapons. When Stark saved the pilot of a damaged F-22 Raptor plane that was pursuing him, Fury realized that he was wrong about Stark. Fury then ordered Coulson to check Obadiah Stane's activities with Stark's financials, and he discovered that Stane was selling the Stark Industries weapons to the terrorists. With the team of agents Coulson went to Stark Industries where he encountered Stark's secretary Pepper Potts who informed him about Stane's involvement in Stark's kidnapping and attempted homicide. Coulson and his men were then attacked by Stane who was now wearing his own armor. However, Stark was able to defeat Stane. Shortly after the battle, Stark and his friend Lt. Col. James Rhodes were taken to a secret S.H.I.E.L.D. base where Coulson told them that Stark should be trained to become a real fighter, and that S.H.I.E.L.D. would provide the teachers. The next morning, Coulson came to Stark Industries Headquarters with the cover story for the incident with the "Iron Man". When Pepper thanked him for his help, he said they'll hear from his agency again. When she tried to say the whole name of the agency, he interrupted her and spoke the acronym "S.H.I.E.L.D." instead. Later, at the S.H.I.E.L.D. Headquarters, Coulson and Fury watched the press conference where Stark publicly revealed that he is Iron Man. That night Fury visited Stark in his Malibu home and informed him of the Avengers Initiative but Stark refused to join Fury's "superhero boy band".

The Ten Rings
"Intel was right about the money, Sir. A Ten Rings cell controls this vessel."

- Garrett to Nick Fury

After Stark's refusal to join the agency, S.H.I.E.L.D. began fighting the Ten Rings. On one occasion, Nick Fury sent a team of U.S. Navy SEALs to board a ship controlled by the Ten Rings in the port of Aden. However, Iron Man suddenly appeared and attacked the terrorists. Though the Seals were outnumbered by the terrorists, Iron Man had no problems with killing all the terrorists and saving the Seals. Later, S.H.I.E.L.D. agent Natasha Romanoff was sent to ruin an operation of the Ten Rings. She boarded the Ten Rings plane and caused its explosion.

Project T.A.H.I.T.I.
"Good Morning Director Fury, I regret to inform you that I’m handing in my resignation. I know you brought me on to Project T.A.H.I.T.I. because you trusted my judgment, and it’s that judgment that’s telling me I can no longer, in my good conscience, let the testing continue."

- Phil Coulson to Nick Fury

In coordination with the Avengers Initiative, Fury started Project T.A.H.I.T.I., an effort to create a medicine that could save a mortally wounded Avenger. Harvesting the bodily fluids from a decaying extraterrestrial corpse at the secret facility called the Guest House, the scientists managed to make the serum that could regenerate the damaged tissue and cure deadly diseases. Six agents who suffered from deadly diseases volunteered for the project and were injected with the serum. The initial tests were partially successful, showing complete physical recovery, but later the experiments went horribly wrong, causing the test subjects to mentally deteriorate, and the project's director Phil Coulson recommended its shutdown. The memories of the patients were erased and they were given the new civilian identities. However, Nick Fury secretly decided to continue with the project.

Day One
"Were you able to locate the Super-Soldier?" "No. We did locate an important clue that could have pointed us in the right direction, but with the ever shifting topography of the Greenland ice sheet, I imagine we'll be starting from scratch again."

- The World Security Council member and Nick Fury

A few months later, Nick Fury and Phil Coulson led an expedition to Greenland in hopes of finding Steve Rogers, the American war hero from World War II. The same day when they found one of the disabled flying bombs from HYDRA's super bomber, the Valkyrie, the World Security Council ordered them to shut down the operation and return to New York City. Twelve hours later, the Council ordered Fury to stop wasting time on what they called "wasteful programs" and focus on reigniting the Tesseract, naming that operation "Project P.E.G.A.S.U.S.". Despite the direct order, Fury decided to continue with his usual activities, and he told Coulson to do the same.

Day Two
"Is there a 50% chance that this "atmospheric disturbance" is just a powerful lightning storm?" "Closer to a 5% chance, Sir." "That still puts it at the bottom of my to-do list. But keep up the good work!"

- Nick Fury and Phil Coulson

The S.H.I.E.L.D. scientists informed Fury that Tony Stark would die in three days of palladium poisoning. They gave him a dose of the Lithium Dioxide that could postpone the inevitable. Also at this time Fury was told that Bruce Banner has passed through US Customs and he orders Jasper Sitwell to track him. Agent Coulson informed Fury of 'atmospheric disturbances' they were picking up in the 'south west' region but Fury decided that wasn't so important.

At the same time, Agent Natasha Romanoff, secretly sent to watch over Tony Stark under the guise of Natalie Rushman, called Fury and informed him of Stark's battle with James Rhodes at his own birthday party. Fury tried to talk with the World Security Council but he was interrupted by an agent who informed him that Tony Stark was located. Fury then left the base, picked up Agent Romanoff, and went to rendezvous with Stark.

Day Three
"What do you want from me?" "What do we want from you? Uh-uh. What do you want from me? You have become a problem, a problem I have to deal with. Contrary to your belief, you are not the center of my universe. I have bigger problems in the southwest region to deal with."

- Tony Stark and Nick Fury

Fury and Romanoff were able to find Stark on the top of the Randy's Donuts restaurant in Inglewood, California. Inside the restaurant Fury confronted Tony Stark for becoming a problem that he had to deal with. As Stark complained about none of the elements being a suitable replacement for the palladium arc reactor that was killing him, Fury told him that he hasn't tried all the elements yet. Agent Romanoff then injected Stark with the Lithium Dioxide, slowing down the poisoning. Later, at Stark's Malibu Mansion, Fury provided Stark the information on the background of the man who tried to kill him, Ivan Vanko. Fury also gave information and materials from his father Howard, one of the founders of S.H.I.E.L.D. Before Fury departed, he assigned Agent Coulson to watch over Stark and keep him in the mansion. Coulson said to Stark that if he tries to leave the mansion, he would taze him and watch Supernanny while he drools on the carpet.

Meanwhile, Jane Foster contacted her mentor, Dr. Erik Selvig, who flew out to New Mexico to help her monitor the atmospheric disturbances. Foster's message was intercepted by S.H.I.E.L.D. and delivered to Agent Coulson.

Day Four
"Sorry for the short notice. Think you can handle things here on your own?" "What could possibly go wrong?"

- Phil Coulson and Natasha Romanoff

When Coulson once again informed Fury about the appearance of a wormhole over New Mexico, Fury agreed to send an expedition led by Coulson himself. Before he departed, Coulson visited Stark in his laboratory, and assisted in his current project of making the new element. Just as he was leaving, Coulson asked Agent Romanoff is she could handle the situation, and she said she would have no problems.

That night at the Stark Expo, Agent Romanoff attended and when Ivan Vanko took control of the Hammer Drones, she went with Happy Hogan to go to Hammer Industries. They broke into the Hammer Industries Headquarters. Hogan took out one enemy combatant while Romanoff dealt with the rest, then proceeded to use a Hammer computer system to restore control of James Rhodes's battle suit to Rhodes. She then retrieved Hammer Industries data before Ivan Vanko's bombs went off.

The same day Agent Couslon arrived at S.H.I.E.L.D. outpost at Roswell, New Mexico to assemble his team of agents.

Day Five
"Why don't you tell me where you received your training? Pakistan? Chechnya? Afghanistan? You know, you strike me more as the soldier of fortune type. Where was it? South Africa? Certain groups pay very well for a mercenary like you. Who are you? One way or another we'll find out what we need to know. We're good at that."

- Phil Coulson to the intruder

Upon arriving in the deserts of New Mexico, Phil Coulson and his team discovered the crater site with the mysterious hammer at the center. Coulson and his men quickly set up a perimeter and a base of operations around the crater. A professor who specialized in the fields of Norse mythology named Elliot Randolph helped Coulson and his group with discovering what the hammer was. At the same time, under orders from Director Fury, Agent Clint Barton was sent to Puente Antiguo assist Coulson.

S.H.I.E.L.D. agents then went to confiscate all of the research about the mysterious wormhole that Jane Foster and her scientific team had collected. They traveled to Puente Antiguo, and despite Foster's protests, Coulson and his men took all of their equipment.

The same night, an unknown man infiltrated Coulson's base and managed to single-highhandedly take out a dozen of S.H.I.E.L.D. agents with various fighting styles. Coulson observed from a distance but not before asking Clint Barton to prepare to take action if necessary. When the attacker tried and failed to lift the hammer, Coulson's men easily captured him. Shortly after, Coulson interrogated the stranger about his identity and his training believing him to be a warrior of some type. However, the stranger refused to answer his questions. Agent Barton advised Coulson to release the intruder and then send agents to follow him. The interrogation was interrupted when Dr. Erik Selvig arrived and informed Coulson that the stranger is Donald Blake, a member of his scientific staff. An agent confirmed Selving's story by running a background check in the computer database and finding a falsified document created by Jane Foster. Though Coulson knew that Selvig was lying, he agreed to free "Donald", only to secretly assign agents to follow Selving and "his friend". Meanwhile, after Ivan Vanko's battle with Tony Stark and James Rhodes at the Stark Expo and the arrest of Justin Hammer, Agent Romanoff returned to the S.H.I.E.L.D. Headquarters to deliver the data obtained at Hammer Industries Headquarters to Director Fury. When she noticed that he doesn't look "so hot", he replied that he hasn't slept much during the last few days. Aware that General Thaddeus Ross and the Strategic Operations Command Center could go hunt Bruce Banner any minute, Fury ordered her to follow Banner's movements. When Romanoff asked why Agent Sitwell wasn't following Banner anymore, Fury replied that he had to send him to New Mexico because of the appearance of an alien object. Romanoff immediately departed for Culver University.

Day Six
"I need you to get to Culver University and put eyes on Dr. Banner. I got word that General Ross is about to make a move on him." "I thought Sitwell was on Banner." "He was, but I had to send him to New Mexico." "Why?" "Because I got an alien object in New Mexico, that's why!"

- Black Widow and Nick Fury

At Culver University, disguised as a student, Agent Romanoff witnessed Bruce Banner being chased by General Ross and the Strategic Operations Command Center; Banner then transformed into Hulk and a battle ensued. She called Fury and barely escaped uninjured. At the S.H.I.E.L.D. Headquarters, Nick Fury informed Tony Stark that while Iron Man was a suitable candidate for the "Avengers Initiative", Stark himself was not. S.H.I.E.L.D. wanted Tony only in a consultant position, to which Stark agreed, on the condition that Senator Stern presented himself and James Rhodes with medals for bravery. When Stark departed, Agent Romanoff showed up, and revealed to Fury that she witnessed Emil Blonsky in action against Hulk and that Army had enhanced him. An hour earlier in New Mexico, an agent discovered the coordinates of another potential crater site that appeared to have an exact signature match to the mysterious hammer. Phil Coulson, Jasper Sitwell and a unit of S.H.I.E.L.D. agents went to investigate, eventually finding a gigantic armor of unknown origin. As the armor slowly approached them, Agent Jasper Sitwell asked Coulson if the armor was one of Stark's. Coulson replied that Stark doesn't tell him anything, and tried to speak with the armor, but the iron giant attacked them. Coulson called Fury and informed him about the "little problem", interrupting his conversation with Agent Romanoff.

Agent Coulson managed to survive the attack from the armor and assembled all uninjured agents to follow it. When the armor attacked Puente Antiguo, Coulson saw "Donald Blake" gaining mysterious supernatural powers. When "Donald" summoned the hammer and defeated the armor, Coulson realized that "Donald" is actually Thor, the Norse God of Thunder and Prince of Asgard. Coulson confronted Thor who offered his services in protecting Earth under the sole condition that Coulson returns all of Jane's research and material back to her. Coulson agreed to Thor's terms and requested that they be debriefed just before Thor flew upwards with Jane in his arms.

Later, Coulson and Clint Barton supervised the transport of the armor to the S.H.I.E.L.D. Headquarters. At the same time Dr. Erik Selvig was taken to a S.H.I.E.L.D. facility where he met Nick Fury. Fury asked Selvig to study the Tesseract, an object of limitless power, and Selvig agreed.

Meanwhile, S.H.I.E.L.D.'s encrypted database was breached by General Thaddeus Ross who wanted to find information on Bruce Banner. An Agent informed Director Fury about the breach and he decided to have a word with the General.

Day Seven
"I don't like it any more than you do, Sir... but we are outmatched. The sooner we accept it the sooner we can fix it... Or the sooner we can stop wasting our time pretending that we can make a difference."

- Natasha Romanoff to Nick Fury

At the Andrews Air Force base in Maryland Fury confronted General Ross, as the Strategic Operations Command Center was preparing to depart in search for Hulk. As Fury warned Ross that his Super Soldier is dangerous and that Captain Blonsky should be removed from the field immediately, Ross replied that he doesn't take orders from him, and then boarded the helicopter and departed. Fury then called his agents and ordered them to find Banner's location and send that information to Agent Romanoff so she could bring in Banner before Ross could capture him.

When Agent Romanoff arrived to Grayburn College it was too late. Banner was already captured by Ross' soldiers and they were taking him away in a helicopter. Romanoff informed Fury about the development of the situation and he ordered her to make sure that Banner did not leave anything for Dr. Samuel Sterns, who he had recently been with, to work on. As she headed up the front steps, she witnessed Blonsky, now transformed into the giant-sized Abomination, emerge from the building. She was buried in rubble, but still managed to make her way upstairs. She stumbled upon Dr. Sterns, whose head and brain seemed to be mutated.

After a brief dialogue with him, during which Sterns identified Romanoff's birth place from a hint of accent in her voice, she shot him in the leg. Romanoff called in a S.H.I.E.L.D. cleanup team, and signaled her location on the roof with flares. She saw the chaos of Abomination and Hulk's battle in the distance. Back at S.H.I.E.L.D. Headquarters, Romanoff confronted Fury, stating that all of the events going on were too much to handle. Fury then called the World Security Council and asked them to increase funding for the agency, expand jurisdiction for his agents, and augment his strategic authority. When they asked what was done about reigniting the Tesseract, he told them about the events of the past week, including how his agents saved Tony Stark's life who then made the new element, formed an alliance with Thor and captured the Destroyer, and saved New York City from being destroyed by General Ross' maniacal enhanced soldier. The Councilmen then replied he would have everything he requires by the end of the month.

The Abomination Problem
"I got it - we send a patsy to sabotage the debriefing." "A patsy?" "Yes. Someone to screw it up. Someone so inept General Ross will refuse to release Blonsky. I could do it. I do a great patsy." "Yes, you do. Your patsy's legendary. In fact, when I think of the word "patsy"..." "Alright."

- Jasper Sitwell and Phil Coulson

When the World Security Council ordered S.H.I.E.L.D. to recruit Emil Blonsky, the Abomination, for the Avengers Initiative, Phil Coulson met with Agent Jasper Sitwell in a cafe to discuss that order. The Council considered Blonsky a war hero, and that he destroyed half of Harlem just because he was attacked by the Hulk. Now S.H.I.E.L.D. had to convince General Thaddeus Ross to free Blonsky.

Both Coulson and Sitwell agreed that releasing Blonsky from the Army's custody would be foolish, and they decided to send a consultant to talk to Ross and convince him not to free Blonsky, someone so irritating and annoying that Ross would simply refuse to free Blonksy. Unwillingly, Coulson decided to send Tony Stark.

A few days later, Coulson and Sitwell met at the same cafe. Their plan worked as they expected because Stark's annoying behavior made Ross so angry that he refused to free Blonsky.

Return of the Ten Rings
"S.H.I.E.L.D. has found us. Wipe them out."

- Richard Frampton

Agent Natasha Romanoff was sent to Moscow, Russia to find the missing Stark Industries technology. In one of the night clubs she attempted to interrogate the illegal arms dealer Mikhail Fjodorov but he was killed by an assassin and Romanoff was forced to escape. At her hotel she was attacked by a team of masked mercenaries, but she defeated them and contacted Sofia, the mysterious woman from the night club who challenged her to a duel. Natasha agreed to meet with Sofia and broke all her contacts with S.H.I.E.L.D. Agent Phil Coulson then sent two agents to search for Sofia.

A few days later, the two agents were killed by Sofia in a sport hall in Sochi. Agent Romanoff was almost killed but she was saved at the last moment by Coulson, who was following a pair of goons working for the arms dealer General Starodoub. Later, Agent Romanoff managed to infiltrate the yacht belonging to Yuri Klementiev, one of General Starodoub's business partners, where she encountered Sofia again, which cost them the life of agent Gennady Markov.

After discovering that Sofia's employer was the billionaire Richard Frampton, Coulson sent Agent Romanoff to infiltrate his headquarters in Vladivostok, where she discovered that Frampton works for the Ten Rings terrorist organization. She also discovered that he has made a Jericho missile, planing to launch it near the border between Russia and North Korea, where its explosion would greatly destabilize the world peace. Romanoff managed to infiltrate the launching area and destroyed the missile. Both Frampton and Sofia were killed in the explosion. A S.H.I.E.L.D. team led by Coulson and Director Fury later came to to clean the area.

Discovery of Captain America
"My God. Base, give me a line to the Colonel." "It's 3 AM, sir." "I don't care what time it is. This one's waited long enough."

- A lieutenant calling a S.H.I.E.L.D. base after finding Steve's body

Nearly 70 years after Steve Rogers' crash landing, a S.H.I.E.L.D. team discovered the remains of the Valkyrie on Greenland. Rogers' body was inside, perfectly preserved in ice. Nick Fury was immediately called, and he informed Phil Coulson about the discovery. They both watched the recovery of the body, which was defrosted and then shipped to S.H.I.E.L.D. Headquarters in New York City. Rogers was kept in a simulated 1942 environment to try and ease him into what was happening.

When Rogers awoke, he quickly realized it was not real and escaped into the streets of a modern New York City. In Times Square, Rogers encountered Nick Fury, who told him that he had been "asleep" for nearly seventy years. Rogers then realized that many of his old friends were very likely dead, including his love interest, Peggy Carter.

Destruction of Project P.E.G.A.S.U.S.
"Coulson, get back to base. This is a LEVEL SEVEN. As of right now, we are at war." "What do we do?"

- Nick Fury and Phil Coulson

When Loki stole the Tesseract from the Joint Dark Energy Mission Facility and escaped along with several enslaved S.H.I.E.L.D. personnel, Director Nick Fury reactivated the Avengers Initiative to counter the threat. Agent Natasha Romanoff was sent to bring in Dr. Bruce Banner, Agent Phil Coulson was sent to retrieve Tony Stark, and Fury himself approached Steve Rogers, all in the hope that together these individuals might combine their respective talents to help with the problem of Loki and the missing Tesseract.

Assembling the Avengers
"We're running the world's greatest covert security network and you're gonna leave the fate of human race to a handful of freaks." "I'm not leaving anything to anyone. We need a response team. These people may be isolated, unbalanced even, but I believe with the right push they can be exactly what we need."

- The World Security Council and Nick Fury

S.H.I.E.L.D. assisted Rogers in his capture of Loki, and then provided a prison on the Helicarrier once Loki had been apprehended. It transpired that Loki had intended to be captured however, a ruse to sow the seeds of discord throughout the ranks of the forces assembled against him. His mind-controlled agents later attacked the Helicarrier to free him, heavily damaging it in the process. The attack became a bitter defeat for S.H.I.E.L.D, although Fury turned one of its defining losses into the motivational push that Stark and Rogers needed. In short order the remaining heroes set off in pursuit of Loki, and began referring to themselves as the Avengers.

Battle of New York
"Director, you're closer than any of our subs, you scramble that jet..." "That is the island of Manhattan, Councilman. Until I'm certain my team can't hold it, I will not order a nuclear strike against a civilian population."

- The World Security Council and Nick Fury

During the Chitauri invasion in New York City, the World Security Council ordered the deployment of nuclear missile to the city in the hope of stopping the invasion. Nick Fury was able to stop a jet carrying a nuke from taking off, but was unable to prevent another. With Fury's help, Iron Man was able to prevent the other missile from detonating over New York City. After the battle, Director Fury gave his report to the World Security Council. Though some of the members were displeased with his actions, he told them that now every world knows about the Avengers.

Resurrection of Phil Coulson
"After New York, you weren't dead for 8 seconds or 40 seconds or whatever they put in your file. You were dead for days." "That's impossible." "It should be, but Director Fury moved heaven and Earth. He had a team of scientists working around the clock using procedures that no good doctor would ever allow."

- Streiten and Phil Coulson

Days after the death of Phil Coulson at the hands of Loki, Nick Fury ordered extreme measures be taken to save him. He was taken to a former World War II bunker called the Guest House. S.H.I.E.L.D. medical staff used a experimental drug to repair the wounded organs at a cellular level.

After at least seven operations, Fury's doctors were actually able to bring Coulson back to life days after he had been killed. The process was extremely, inhumanly agonizing for Coulson, who begged the doctors to let him die.

During the process, they altered some of his memories with a robotic-assisted neural micro-surgery, to make him believe that he was revived in Tahiti, in order to cope with the pain he felt and to make him less suicidal, as he wanted to die due to the intense agony he was experiencing. S.H.I.E.L.D. Doctor Streiten maintained that the methods used to restore Coulson to life were unethical and felt that they should have let him die. The details of his revival are only available for agents with Clearance Level 10 or above.

Dr. Streiten was reluctant to release him back into active duty given the horrific nature of his recovery and was astonished to realize that Coulson was unaware of the truth of his survival. Agent Maria Hill told Streiten that Coulson could never know the truth.

Item 47
"Agent Blake, I'd like you to meet Claire Wise and Benjamin Pollack. Benjamin here is the latest addition to the S.H.I.E.L.D R&D think tech. He's gonna help us reverse engineer some of the alien tech."

- Jasper Sitwell to Felix Blake

When two bank robbers, Claire Wise and Benjamin Pollack, come into possession of a Chitauri weapon, Felix Blake sent Jasper Sitwell to kill them and retrieve the weapon. Sitwell tracked them to a motel and stayed in the room next to theirs. He disturbed them with loud music and Benny went to investigate. Sitwell attacked Benny, who warned Claire of the ambush. Claire then attacked Sitwell with the Chitauri weapon. During the struggle, the gun destroyed most of the room, but was broken in the process. Sitwell then tied up Benny and Claire, but decided not to kill them when he discovered that the gun was working because Benny, who was a scientist, had repaired it. Seeing a great potential in the couple, Sitwell recruited Benny and Claire in S.H.I.E.L.D. as special agents, much to Blake's disappointment.

Fury's Secret Bases
"Secret base, huh? Sounds just like Fury."

- John Garrett

After the Battle of New York, now always on the alert, Nick Fury set up several secret bases around the globe, manned only by the most loyal S.H.I.E.L.D. agents, the Koenig brothers. One of the brothers, Eric Koenig, referred to his base as "Providence". Another named Billy was stationed at the Playground.

Project Insight
"This is Project Insight. Three next generation Helicarriers linked to a network of targeting satellites." "Launched from the Lemurian Star." "Once we get them in the air they never need to come down."

- Nick Fury to Captain America After the Avengers' victory and departure, S.H.I.E.L.D. was given more resources than they ever had before in order to make sure that if a threat similar to the Chitauri attacks Earth, they would be prepared. With more funds to invest in homeland security, the leaders of S.H.I.E.L.D. started "Project Insight", a security network formed by three heavily-armed Helicarriers to protect the Earth. In S.H.I.E.L.D.'s plans, the Helicarriers would proactively strike out against potential threats before they actually happened. However, HYDRA's undercover operatives in S.H.I.E.L.D. intended to use the Helicarriers to exterminate any person that would pose a threat to HYDRA's plans of world domination. Soon, the crews of all three Helicarriers were composed entirely of HYDRA's undercover agents.

The Phantom Terrorist
"I've compiled a Mandarin database for you, sir, drawn from S.H.I.E.L.D., FBI, and CIA intercepts."

- J.A.R.V.I.S. to Tony Stark

In 2012, a series of bombings occurred around the world, some of them in the American military bases. A man calling himself the Mandarin began appearing in video broadcasts, claiming responsibility for those terrorist attacks. S.H.I.E.L.D began collecting Intel on the bombings, and the collected informations were later used by Tony Stark in his fight against Aldrich Killian and the Advanced Idea Mechanics.

Foundation
"I assembled this team!"

- Melinda May to Phil Coulson

Some time after the battle of New York, Melinda May assembled a team of agents to keep an eye on Phil Coulson's recovery for Nick Fury. Coulson however believed he had set up the small, highly trained team of agents to tackle the cases that have not been classified yet. The team originally consisted of Coulson, May, Grant Ward, Leo Fitz and Jemma Simmons. They later recruited Skye to the team as a consultant and took part in missions in Los Angeles and Peru.

The Asset
"We could've worked with you on this." "S.H.I.E.L.D.? S.H.I.E.L.D. is just as guilty of the same thing! Experimentation without thought of consequence! Your search for an unlimited power source - brought an alien invasion."

- Phil Coulson and Franklin Hall

In 2013, S.H.I.E.L.D. searched for one of its assets, Dr. Franklin Hall, who was kidnapped by his former research partner and CEO of Quinn Worldwide named Ian Quinn. His soldiers used a gravity device on the S.H.I.E.L.D. convoy that was transporting him. Quinn wanted to use Hall to take control of the planet's gravity by building a giant Gravitonium generator. Phil Coulson and his team headed to Malta and Skye volunteered to infiltrate Quinn's mansion during his party so that Coulson and Ward could rescue Hall. Skye tricked Quinn into believing she is betraying S.H.I.E.L.D. for Rising Tide to get his guard down. However, Coulson discovered that Hall perpetrated his own escape and wanted to destroy the massive device as believed he is in the right. Coulson warned him that doing so would end up killing millions. There is a violent disagreement which lead to Coulson being forced to leave Hall to die as he fell into the middle of the generator. Coulson ordered that the Gravitonium be placed under high security and off the books in the Fridge.

Centipede Project
"We didn't cut off the head of the Centipede. Whoever sponsored that little experiment is still out there, among other things."

- Phil Coulson to Skye

The Centipede Project first came to the attention of Coulson's Team in Los Angeles but the rest of S.H.I.E.L.D. learnt about them when Index-registered pyrokinetic Chan Ho Yin was kidnapped from his Hong Kong apartment by a woman named Raina, who worked for the Centipede Project. Chan was brought to a nearby lab where Debbie managed to harvest the fire-resistant platelets in Chan's blood. The platelets allowed the Extremis element of the Centipede Serum to be stabilized without the explosive after-effects. Having gotten what they needed from him, Debbie ordered Chan be drained, killing him.

But before that could happen, Chan was released by a S.H.I.E.L.D. extraction team led by Phil Coulson and Agent Quan Chen. Unfortunately, Chan (Now going by the name "Scorch"), was tired of S.H.I.E.L.D.'s interference in his life, and killed Quan. Chan then confronted Debbie and Raina. Raina abandoned Debbie, leaving her to be incinerated by Chan. Raina escaped, but the lab was destroyed when Chan detonated from an Extremis overdose.

Before the destruction of the lab, S.H.I.E.L.D. consultant Skye managed to extract a few files from the building's mainframe, enough to give S.H.I.E.L.D some new leads on their activities.

Battle of Greenwich
"What are you doing?" " Out of sight, out of mind. That's why we're here. Keep everything under control."

- Leo Fitz and Grant Ward

S.H.I.E.L.D. was not present during the Battle of Greenwich but arrived for cleanup after the event. The pieces of Dark Elf technology left behind after the battle were collected by S.H.I.E.L.D., and the damage was cleaned up.

Kidnapping of Phil Coulson
"S.H.I.E.L.D.'s gonna find me before you break me."

- Phil Coulson to Raina

Edison Po was broken out of Havenworth Federal Penitentiary by a squadron of Centipede Soldiers. They took him to the new Centipede lab in Oakland, California, where Raina updated him on the project's status. Po determined that S.H.I.E.L.D. presented a threat that needed to be taken care of. He set a trap for S.H.I.E.L.D. with three Centipede soldiers laying in wait.

However S.H.I.E.L.D. had recruited the Centipede Serum-powered Michael Peterson. Peterson's presence turned the tide against the Centipede soldiers, but it also gave Po and Raina the inspiration for a plan of action.

Raina kidnapped Michael's son Ace and threatened to have him killed if Peterson didn't obey her instructions. Believing that Centipede wanted to exchange Peterson for his son, Phil Coulson accompanied Peterson to the exchange site in Long Beach, California. Seeing no other way to save his son, Peterson betrayed Coulson to Raina. After seeing to his son's safety, Peterson tried to make up for his actions by returning to rescue Coulson, but he was seemingly killed in an explosion.

Raina escaped the scene with Coulson by way of helicopter. Upon leaving the scene, Raina explained to Coulson that their true interest was in the nature of Coulson's mysterious revival after his "death" before the Battle of New York, as this is seemingly the key to "Stage Three" of the Group's plans. S.H.I.E.L.D. left no stone unturned in their search for Coulson. A sting operation performed by Coulson's Team under the direction of Agent Victoria Hand netted the international criminal Vanchat, who had had dealings with Centipede Project in the past. Between the intel gained from Vanchat, as well as an independent study of Vanchat's finances by S.H.I.E.L.D. consultant Skye, S.H.I.E.L.D. determined the locations of several Centipede operations around the globe, as well as Coulson's location in the Mojave Desert.

S.H.I.E.L.D. teams struck simultaneously at multiple Centipede locations across the globe, Coulson's team headed to Mojave to rescue Coulson. After subduing a cadre of Centipede-powered soldiers, Coulson was located and Raina taken into custody.

The Guest House
"This is S.H.I.E.L.D. There are always secrets." "That's my fear, sir. Your file is filled with secrets experimental drugs; unknown surgical procedures we've never even heard of."

- Phil Coulson and Jemma Simmons

After the events of Phil Coulson's kidnapping, S.H.I.E.L.D. became interested in finding the Clairvoyant. Coulson's Team boarded a train in Italy on which a Cybertek security group were shipping a package to Ian Quinn. Skye and Leo Fitz tracked the Cybertek package to Quinn's mansion, where, in the basement, Skye was confronted by Quinn, who revealed that Michael Peterson was alive, having been kept in a Hyperbaric Chamber. The Cybertek package contained a high-tech prosthetic leg which Quinn then fitted onto Peterson's amputated right leg. Quinn then shot Skye twice in the stomach and left her for dead while Peterson escapes. S.H.I.E.L.D. then raided the mansion and Quinn was arrested. Skye; however, was left near death and was temporarily sustained by being placed into Peterson's hyperbaric chamber.

Skye was rushed to a S.H.I.E.L.D. Trauma Zentrum to save her life. The doctors were only able to stabilize her, which forced Coulson to bring her to the S.H.I.E.L.D. location where he was revived. Agents John Garrett and Antoine Triplett boarded the Bus in order to claim Ian Quinn but instead helped Coulson's team in recovering the drug that revived him from the "Guest House", which was a former top-secret storage facility at a classified location that was previously affiliated with S.H.I.E.L.D. Coulson, Grant Ward, Garrett and Fitz entered and found the place rigged with explosives after they took out the only two guards. Fitz was able to find the drug, while Coulson found a room marked T.A.H.I.T.I. Fitz got back to the Bus to deliver the drug while Coulson explored the room. Inside, Coulson found more of the drug as well as discovering that the drug is coming from the upper half of a blue-skinned humanoid corpse.

The team was able to get out before the facility exploded, but Coulson raced to prevent Fitz giving Skye the drug, based on what he has seen in the T.A.H.I.T.I. room. Fitz managed to give the drug to Skye quickly enough to save her.

Hunt for Lorelei
"You are of S.H.I.E.L.D.?" "Yeah...?" "I am Lady Sif, of Asgard. Your world is in grave danger."

- Sif and Grant Ward

Coulson's team was ordered to investigate an energy reading in the desert consistent with the imminent arrival of an Asgardian. They encountered Lady Sif, who had come to Earth seeking Lorelei, an Asgardian criminal who had traveled to Earth seeking to enslave humanity. Phil Coulson's team and Sif traveled to a biker bar Lorelei was using as a hideout, but after a short battle, Lorelei enthralled Agent Grant Ward and escaped with him. The pair traveled to Las Vegas, where Lorelei learned much of Earth's governments from Ward, and used this information to formulate a planetary takeover. However, Ward informed Lorelei of the threat posed by his team, and together, the two infiltrated the Bus in an attempt to kill them. Lorelei enthralled Leo Fitz, who in turn isolated the rest of the team while Ward took control of the plane. However, Lorelei's plans were ruined before they could even begin, as she underestimated the threat posed by Melinda May, who distracted Ward from Sif as Lorelei dueled her. Sif bested Lorelei in combat, silencing her with the collar. The enthralled were freed from Lorelei's control immediately.

Sif took Lorelei back to Asgard, where she returned to imprisonment.

Search for the Clairvoyant
"Think about it. The Clairvoyant only knew you'd be at Quinn's villa..." "After I dropped a tracker. And the only thing he's had trouble seeing is what happened to you after you died." "Because Director Fury wouldn't release that file to anyone." "No..." "The Clairvoyant doesn't have abilities. He has security clearance. He's an agent of S.H.I.E.L.D.!"

- Phil Coulson and Skye After Agents John Garrett and Antoine Triplett were attacked in a S.H.I.E.L.D. safehouse by former S.H.I.E.L.D. Trainee Michael Peterson (now going by the name Deathlok), Phil Coulson invited them, Victoria Hand, Felix Blake and Jasper Sitwell to the Bus to hunt for the Clairvoyant. The agents were split into teams so that they could pursue leads on different Clairvoyant candidates. Before Sitwell could take part in the mission, he was ordered by Director Nick Fury to go to the Lemurian Star.

Felix Blake and Melinda May were sent to a Tranquility Bridge nursing home to search for Thomas Nash who was a catatonic man who claimed to be a psychic. The pair however encountered Deathlok and Blake was critically injured by him. Before Deathlok escaped, Blake managed to tag him with Tag Rounds. S.H.I.E.L.D. concluded that Nash is the Clairvoyant because of Deathlok's presence along with the falsifying of his nursing home records. A S.H.I.E.L.D. team converged on Deathlok's next location which was an abandoned horse racing track. Meanwhile Triplett and Jemma Simmons stayed behind at the Hub with Hand.

The team encountered Deathlok again, but he fled into the sewers soon after being engaged. The team however discovered a hidden room where Thomas Nash who was a vegetative man on life support who had to speak through a computer, was hiding. Nash surrendered and boasted that as the Clairvoyant, he would always be watching them. When he said that Centipede Project will kill Skye, Ward shot him in the chest, killing him. Ward was detained for his actions and accused by Coulson for working with the Clairvoyant by shooting Nash to misdirect away from the Clairvoyant's true identity.

The Lemurian Star
"Target is a mobile satellite launch platform, the Lemurian Star. Setting up their last payload when pirates took 'em, 93 minutes ago."

- Brock Rumlow

After the arrival of Jasper Sitwell to the S.H.I.E.L.D. ship Lemurian Star, a group of pirates led by Georges Batroc attacked the ship. Captain America, Black Widow and STRIKE were sent to the mobile satellite launch platform to retake command and free its hostages, when it was setting up its last payload in the Indian Ocean. The team successfully infiltrated the ship and rescued the hostages, however unbeknownst to Captain America, Black Widow was sent to get valuable data about S.H.I.E.L.D. for Director Nick Fury. Batroc escaped but was later captured in Algiers, Algeria and interrogated by another S.H.I.E.L.D. team.

Attack on Nick Fury
"Nick Fury was murdered in cold blood. To any reasonable person, that would make him a martyr, not a traitor." "You know what makes him a traitor? Hiring a mercenary to hijack his own ship."

- Alexander Pierce and Rockwell

After receiving the files from the Lemurian Star, Nick Fury discovered that the data was unable to be accessed. Fury reported this to Alexander Pierce, who had just been speaking with the World Security Council about whether or not to let Fury continue to run S.H.I.E.L.D. Afterwards, while driving through Washington, D.C., Nick Fury was attacked by mercenaries disguised as the police. After getting the systems back online on his SUV he managed to escape but was then stopped by a surprise attack from the Winter Soldier. Although his car was totaled and he was badly injured he managed to escape using the Mouse Hole device and hid in Steve Rogers' apartment.

When Rogers arrived at his apartment he found Nick Fury sitting on his couch. He told Rogers that S.H.I.E.L.D. is compromised and not to trust anyone. Fury gave Rogers the USB with the data and was then shot suddenly three times in the chest from a nearby rooftop. Rogers gave chase to the gunman but eventually lost him. Fury was taken to hospital but after some time he was pronounced dead. Maria Hill took care of the body.

The Big Revelation
"S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA."

- Captain America After Captain America and Black Widow found Arnim Zola's consciousness in a S.H.I.E.L.D. facility now in a computer body, the digital Zola revealed that HYDRA grew inside S.H.I.E.L.D. with the intention of creating the fascist new world order. When the short-range missile launched by S.H.I.E.L.D. destroyed the base, the STRIKE team came to find their bodies, but the two fugitives were already gone.

Joining forces with Sam Wilson, Cap and Natasha kidnapped the HYDRA mole Jasper Sitwell and forced him to reveal HYDRA's plans. Sitwell revealed that HYDRA intended to use the Project Insight Helicarriers to kill 20 million people who would pose a threat to HYDRA. However, the trio were attacked by the HYDRA assassin known as the Winter Soldier, and later captured by the STRIKE team. Thanks to Maria Hill, Rogers, Romanoff and Wilson were saved, and taken to a secret base where Nick Fury was recovering from his wounds.

Battle at the Triskelion
"If you launch those Helicarriers today, HYDRA will be able to kill anyone that stands in their way...unless we stop them. I know I'm asking a lot, but the price of freedom is high; it always has been. And it's a price I'm willing to pay. And if I'm the only one, then so be it. But I'm willing to bet I'm not."

- Steve Rogers to S.H.I.E.L.D. agents at the Triskelion

Though Fury objected to Rogers' plan to take down S.H.I.E.L.D. to expose HYDRA's existence to the world, all others agreed, because HYDRA's infiltration was too deep. After infiltrating the Triskelion, they posted all of S.H.I.E.L.D.'s classified files on the internet, exposing the truth. They succeeded in preventing three Helicarriers from killing innocents by having them target each other. During all this, an encrypted message was sent out saying "OUT OF THE SHADOWS AND INTO THE LIGHT" and the word "HYDRA". This was a trigger message to all HYDRA sleeper agents that the time for hiding themselves was over. In the ensuing internal conflict HYDRA attempted to pre-emptively take over several S.H.I.E.L.D. installations, including the Hub, the Treehouse and S.H.I.E.L.D. Academy. They were successful in some of these locations, but were denied the Hub by the actions of Victoria Hand and Coulson's Team who swiftly identified most of the traitors. The crew of the aircraft carrier Iliad managed to defeat the HYDRA infiltrators, but suffered heavy casualties. Subsequent to this, S.H.I.E.L.D. was in disarray - Fury was believed dead, Pierce and Sitwell dead and disowned, Hill abandoned the organization, Garrett was arrested, Blake was in hospital and as far as any in the Hub could tell, Hand and Coulson were the highest-ranking agents left. However the situation worsened further when Agent Grant Ward killed Hand and released Garrett.

Save What You Can
"You were right all along. Having all this out there in the world makes it too dangerous, and now there's no one left to protect it." "There's us. We were lucky enough to make it through. The Triskelion, the Hub, those battles are just the beginning of this war. HYDRA's out there now, but at least our team's still intact. We can fight them, and we will."

- Skye and Phil Coulson

After this first insurrection, only four S.H.I.E.L.D. installations were confirmed to have resisted HYDRA (the Triskelion, the Hub, the Fridge, the Cube), and the Treehouse and another unnamed base in East Africa were confirmed to have been taken over by HYDRA. The aircraft carrier Iliad was controlled by S.H.I.E.L.D. agents led by Robert Gonzales, but they had no contact with the rest of S.H.I.E.L.D. One of the bases that had resisted the initial insurrection did not last long as Grant Ward and John Garrett raided the Fridge, acquiring various weapons that the Slingshot supposedly had fired into the Sun (in reality, each item had been kept and catalogued) and freed the prisoners held there. The U.S. government declared S.H.I.E.L.D. a terrorist organization and sent Colonel Glenn Talbot to take the agents at the Hub into custody. Phil Coulson, the ranking agent on-site, decided to order the base's evacuation before Talbot's forces could arrive and went on the run. After taking his team on the Bus and erasing their identities, Coulson received a signal from Nick Fury (who he thought was dead) which led him to the top-secret Providence Base.

Outlawed
"We have no jurisdiction now that S.H.I.E.L.D.'s been labeled a terrorist organization."

- Jemma Simmons to Leo Fitz

Although the Black Widow testified at a committee hearing on the events at the Triskelion and insisted S.H.I.E.L.D. had done its best, the U.S. government declared S.H.I.E.L.D. a terrorist organization and many former agents were now to be considered fugitives. Phil Coulson's team evaded capture and erased their identities. Maria Hill took a job at Stark Industries where she would have protection through Tony Stark's network of top lawyers.

Once inside the Providence, Coulson's team could take some rest, but not for long. The Fridge facility was attacked by HYDRA with devastating results. The most dangerous items and weapons S.H.I.E.L.D. has ever recovered were now controlled by HYDRA and all the inmates were liberated. Pretending that he was still a loyal S.H.I.E.L.D. agent, Grant Ward came to the Providence base, staying there with Agent Koenig and Skye while the rest of Coulson's team went to Portland to hunt Marcus Daniels, one of the escaped inmates from the Fridge. When they left, Ward killed Koenig and flew off on the Bus with Skye. When Coulson and his agents returned, the base was empty.

Hunt for the Centipede
"We're not bringing the band back together again, Coulson. It's over. There is no S.H.I.E.L.D. anymore." "Well, not officially." "Look, I get it, okay? You have to take Ward and Garrett down. But don't act like it's some officially sanctioned mission. It's a personal vendetta, and when it's done, you should walk."

- Maria Hill and Phil Coulson

Meanwhile, the USAF contacted Maria Hill, the former Deputy Director of S.H.I.E.L.D., and convinced her to lead them to the Providence base. Led by Colonel Glenn Talbot, a team of soldiers broke into the facility. A the Colonel was interrogating his agents, Coulson spoke with Hill about Ward's betrayal, convincing her to help him escape from Talbot's custody. The S.H.I.E.L.D. agents attacked Talbot and his men, overpowered them, boarded the S.H.I.E.L.D. Jump Jet, and escaped. Later, in Los Angeles, the team confronted Ward and saved Skye, though Ward managed to escape with the Bus. Later, at the hotel, Maria Hill tried to talk Coulson out of continuing his hunt for the Centipede Group, as S.H.I.E.L.D. was, in her opinion, no longer existing, but Coulson still decided to continue his mission. A few days later, Coulson's team infiltrated a Cybertek facility, stealing a file on Project Deathlok. In Havana, Cuba, Leo Fitz and Jemma Simmons were captured by Ward and Garrett, while the rest of the team was ambushed at the Barbershop Headquarters. The ambush was unsuccessful, but Fitz and Simmons, trapped in a locked room on the Bus, were ejected into the ocean.

The Final Victory
"It'll be just the four of us. We'll be outmanned and outgunned. But Fury always said... a man can accomplish anything when he realizes he's a part of something bigger. A team of people who share that conviction can change the world. So, what do you say? You ready to change the world?" "No. But I'm ready to kick some ass." "That works, too."

- Phil Coulson and Melinda May

Using a tracker Leo Fitz and Jemma Simmons were able to plant on the Bus, Coulson and his remaining teammates attacked the Cybertek Manufacturing Facility in New Mexico. Meanwhile, Simmons and Fitz were saved by Nick Fury who took them both to the Playground, one of his secret bases. Later, Fury joined Coulson and helped him defeat John Garrett and his Centipede Soldiers. After the battle, Fury appointed Coulson as the new Director of S.H.I.E.L.D. and gave him the Toolbox so he could rebuild the organization. Coulson and his team then went to the Playground base, where they were reunited with Simmons and met Agent Billy Koenig.

Robert Gonzales' S.H.I.E.L.D.
"For a while there, it all went to hell. It was bad. But now Bobbi and I work for an organization, an outlier that came out of the wreckage from what Fury left."

- Alphonso Mackenzie

In the meantime, Agent Robert Gonzales managed to assemble some S.H.I.E.L.D. agents and scientists, the survivors of the battles on the Iliad and the S.H.I.E.L.D. Academy, including Bobbi Morse, Alphonso Mackenzie, Isabelle Hartley, Tomas Calderon, and Anne Weaver. Using the aircraft carrier Iliad as his mobile headquarters, he successfully reorganized these remnants and became the leader of the group, not knowing about Fury's survival. Once he found out about Phil Coulson's faction, and not knowing about Coulson's appointment and mission, Gonzales decided not to accept Coulson's authority, and instead sent Agents Morse, Hartley, and Mackenzie to infiltrate Coulson's organization and gather intel. Once they found out about the Toolbox, Gonzales started believing that he could use it to find the objects and people of terrifying power hidden across the world by Nick Fury, so he ordered his agents to retrieve it.

Starting From Scratch
"What is it?" "Toolbox. To help you build it back up." "You want me to start over, rebuild S.H.I.E.L.D." "From scratch. Take your time, and do it right."

- Phil Coulson and Nick Fury

Now possessing merely a shadow of its former strength, S.H.I.E.L.D. had to confront threats posed by HYDRA from the organization's new headquarters at the Playground base. Phil Coulson became a busy man with S.H.I.E.L.D.; between the traitors, those who chose not to return, and those who chose private security, Coulson found it hard to recruit members. He chose three mercenaries, Idaho, Lance Hunter, and former agent Isabelle Hartley, to join his team on missions, and a mechanic named Alphonso Mackenzie to assist Billy Koenig in the Playground. The brain damage of Leo Fitz was severe, Jemma Simmons was not with them, and Grant Ward was suicidal and in isolation, refusing to speak to anyone but Skye. Simmons was ordered by Coulson to infiltrate HYDRA's science division acting as his source within HYDRA. Coulson also had Bobbi Morse infiltrate HYDRA in its security division and to keep an eye on Simmons.

The first team mission had May, Triplett, and Skye act as back-up for the mercenaries while they attempted to purchase information on an 0-8-4 that a former agent once guarded. The negotiation failed when the Absorbing Man killed the agent and took the file.

New Battles
"If we went down today, we'd probably be down for good. But now we have a chance to survive. We have soldiers willing to sacrifice, but they need weapons. The enemy has the advantage. We need one of our own. Disappear. Become ghosts. That's how we have to live now, in the shadows, to save people even when they don't know it, don't want it."

- Phil Coulson to Alphonso Mackenzie

After Coulson confronted Glenn Talbot, he sent the six on a two-pronged mission: obtaining the Obelisk and a Quinjet. The Absorbing Man attacked and killed Hartley and Idaho to get the Obelisk for HYDRA, while Coulson's team escaped in a cloaked Quinjet. Despite this loss the team was able to capture and secure Carl Creel, thanks to assistance of Fitz and Mackenzie, dropping him off in the custody Glenn Talbot. They were able to equip the Bus with the cloaking technology from the Quinjet.

Coulson then tried to recruit Agent 33, but was too late before HYDRA captured her. Coulson, after receiving intel from Simmons, tried to rescue the gifted-scientist Donnie Gill from HYDRA. However, Coulson and his agents were unable to stop HYDRA from triggering Gill's brainwashing program. Hence, Skye was forced to shoot Gill off the side of the Maribel del Mar. Though they do not know if Gill survived, Coulson's team was able to confiscate HYDRA's cargo on the ship.

Coulson then had S.H.I.E.L.D. continue to look into the alien symbols. He then learned of painting that survived a fire at a church in Miami. The painting had been carved on by former S.H.I.E.L.D. agent and Project T.A.H.I.T.I. patient Lewis Seaver, who was killed in the fire by Sebastian Derik. Coulson and May then infiltrated the fundraiser to get their hands on the painting; however, Coulson and May encountered General Talbot, who was actually the HYDRA agent Sunil Bakshi in disguise. Coulson and May eventually escaped with the painting.

New Enemies
"S.H.I.E.L.D.'s becoming a problem. Do we know who's in charge?" "I'm afraid not."

- Daniel Whitehall and Sunil Bakshi

HYDRA later sent a team of mercenaries to attack a United Nations summit posing as S.H.I.E.L.D., killing and injuring many people with Glenn Talbot among the injured. When Senator Christian Ward planned to make a police force to capture any S.H.I.EL.D agents, Coulson, in an attempt to keep his allies safe, made a deal with Christian. If the Senator called off the manhunt, Coulson would give him his brother, Grant Ward. Knowing this would save his reputation and his election campaign, Christian agreed. Later Hunter, Morse, and May told Coulson that Julien Beckers' offering of his country as a safe haven for S.H.I.E.L.D. agents was a ruse to draw them in. While Agents Morse, May, and Hunter managed to defeat the HYDRA agents, they lost six of their own in the trap.

Search for the City
"Now they need the lock, a temple inside the city." "Any idea where this temple is?" "Glad you asked. No. But it's in the city, and we now know where that is. Even better, HYDRA doesn't."

- Skye, Jemma Simmons, and Phil Coulson

When Coulson saw news on the ritualistic murder of artist Janice Robbins, he recognized her as Rebecca Stevens, a Level 6 agent from the Triskelion. Coulson and Skye then investigated and figured out that she was a T.A.H.I.T.I patient due to her paintings which contained the Words of Creation. Robbins' corpse was taken to the playground where Dr. Simmons confirmed that she was a T.A.H.I.T.I. patient and was killed by a fellow T.A.H.I.T.I. patient. Knowing that they needed more information, Coulson had himself put back into the Theta Brain-Wave Frequency Machine to learn the names of the T.A.H.I.T.I. patients. Coulson then found out that there were two left from the six patients; Sebastian Derik and Hank Thompson (former agent Cameron Klein). At the same time, Antoine Triplett and Bobbi Morse followed Grant Ward to Atlanta but they gave up after discovering that he was wired to lots of C-4. Later, in Boston, Melinda May, Triplett, Lance Hunter and Morse entered the pub owned by HYDRA, discovering Sunil Bakshi who was left there tied up by Ward.

Meanwhile Coulson went after Thompson but was subdued by Derik. However, Coulson and Thompson were then able to free themeselves and stop Derik. Coulson then found out the secret of the symbols which were actually blueprints of a city. Coulson told all his agents of their new mission; find the city before HYDRA. While Melinda May stayed behind to be in charge of the Playground, Phil Coulson took Leo Fitz, Antoine Triplett and Skye to Hawaii. He gave each a particular mission, then had the Bus take them to Australia. At Laura Creek, there was a satellite relaying station that was easier to infiltrate than the Kaena Point Air Force Base in Oahu. The assignments Coulson gave earlier was to cause an EMP blackout at that base which would cause the one at Laura Creek to be used as back-up. Coulson wanted their satellites hacked so he could find the city that matched the Words of Creation. However, while there, the team was ambushed by HYDRA and Triplett was seriously shot.

An unknown man suddenly appeared and offered to save Triplett's life. Revealing himself as Skye's father, he severed one of Trip's arteries, holding Trip's life in his hands. After talking to Coulson about the city, the temple, the Diviner, and Skye, though he insisted on calling her Daisy, the man escaped so he could rejoin HYDRA. The agents then took Triplett back to the Bus, and the computers soon found the location of the city in Puerto Rico.

Battle for the Kree City
"Here's what we know. HYDRA's on the move. They have the Obelisk and an expert who knows how to use it. We can't let that happen, obviously."

- Phil Coulson

With the location of the mysterious city finally known, Coulson split his agents into two groups. One group, consisting of Agents May, Skye, Hunter, and Triplett, would go to Canada to help the Koenig brothers in protecting Raina, while the other, consisting of Agents Morse, Mackenzie, Fitz, and Simmons, and which he himself would lead, would go to Puerto Rico to look for the city.

In Vancouver, the agents had a confrontation with a group of HYDRA operatives led by Agent 33. When Raina learned from Skye that Whitehall had the Obelisk, Raina tried to surrender to HYDRA; but May prevented that from happening. Raina was then taken to the Bus, but during the flight to Puerto Rico, the plane was surrounded with four HYDRA quinjets. Grant Ward and a team of HYDRA agents then boarded the Bus, forcing May to hand over Raina and Skye. Once the plane with Ward, Raina, and Skye departed, the remaining quinjets tried to destroy the Bus, but May managed to pilot the plane to safety.

Meanwhile, Coulson and his team discovered the entrance to the alien city beneath Castillo San Cristóbal, an old fort in San Juan. When Mackenzie got down there, he was possessed by some invisible force. When he was hoisted up, he attacked his colleagues and Morse electrocuted him. He then fell back into the the shaft. Later, the Bus landed near San Juan, and the teammates reunited, preparing to attack the Ponce de León Theater where HYDRA's operatives were drilling a hole to the Kree City. The agents successfully infiltrated the theater, attacking and killing several HYDRA operatives, including their leader, Daniel Whitehall. However, when they entered the Kree City, planing to destroy it, Agent Skye entered the temple in the center of the city. Agent Triplett defused the bombs, but later died while trying to save Skye from the mysterious substance that engulfed her in a cocoon. As the temple started shaking from an earthquake, Coulson found and saved Mack, bringing him back to the surface.

Cutting off the Heads
"We did not fail! Trip prevented a disaster, and Whitehall's dead. We cut off the head. And while HYDRA scrambles for a new one, I will crush them! I'm gonna make someone pay... whoever the hell it is."

- Phil Coulson

Upon the return from the Kree City, Skye was quarantined in the Playground in order to see if she harbored any ill effects from her time underground. Meanwhile, Jemma Simmons and a team of scientists stayed in San Juan to map the Kree City. They were attacked by a humanoid creature that turned out to be a transformed Raina. Simmons hit Raina several times, but she escaped.

In the meantime, Coulson made a deal with General Glenn Talbot about giving him Sunil Bakshi in exchange for Talbot's assistance in taking down the remaining HYDRA forces. Unbeknownst to Bakshi, they planned to organize a fake escape to see where Bakshi would go. After the escape, Bakshi was decieved by Agent Hunter into thinking one of the HYDRA leaders was making a move to kill the others. With this Octavian Bloom ordered the other leaders killed. In the resulting chain reaction, most of the HYDRA leaders died. Bloom was then promptly shot and killed and Bakshi was recaptured by Agents Hunter and Morse. Coulson later secretly sent Agent Michael Peterson to search for Doctor List, one of the few surviving heads of HYDRA.

The Gifted and the Enhanced
"Sir, these people are on the Index, but they are not exactly gifted." "They were considered highly dangerous, larger part of the Index functions as more of a watch-list."

- Bobbi Morse and Phil Coulson

When the Asgardian warrior Lady Sif appeared in Portugal, Coulson and a few agents traveled there to find out what was she doing on Earth. To their surprise, she did not recognize them. Soon they discovered she was following a dangerous man, who turned out to be an extraterrestrial just like Sif. They found and captured him in the Portuguese city of Chaves, the same place where the HYDRA leader Daniel Whitehall discovered the Obelisk during World War II.

Back in the Playground, the stranger revealed himself as a Kree called Vin-Tak. His mission was to find the Inhumans recently activated by the Terrigen Mist in the Kree City beneath San Juan. As a sign of good faith, he used his Truncheon to restore Sif's memories, and they questioned Skye about what happened in the temple. When the base started shaking they realized Raina wasn't the only Inhuman activated that day. When Sif asked Coulson to let her take Skye to Asgard, he said no and Vin-Tak attacked him. May took Skye to Vault D while Morse and Mackenzie tried to stop Vin-Tak. Mackenzie was defeated but Morse distracted Vin-Tak long enough for Leo Fitz to fire the Destroyer Armor Prototype Gun at him. When Sif entered Vault D, Skye shot herself with May's I.C.E.R. which finally convinced Sif that Skye could be handled by her own team. Later, when Lance Hunter confronted Mackenzie and demanded full disclosure about his secret mission with Morse, Mackenzie knocked him unconscious. Mackenzie took Hunter to a S.H.I.E.L.D. Safe House where he left him locked and handcuffed.

A few days later, while Jemma Simmons was analyzing Skye's blood, Phil Coulson and Melinda May decided to place Skye on the Index. Coulson then asked May to request the help of Andrew Garner, her ex-husband. May brought Garner to the Playground and he boarded the Bus where Skye had made a residence. Meanwhile, Coulson and Morse went to the Brynmore Psychiatric Facility. One dangerous patient, David Angar, was freed from the facility by Skye's father, Calvin Zabo, and his team of enhanced people from the Index. Coulson and Morse then followed Zabo to Manitowoc, Wisconsin. At the high school stadium, Coulson was surrounded by members of Zabo's team, when May arrived with Skye at gunpoint. Suddenly, an unknown eyeless man appeared and teleported Zabo away. Coulson and his agents then easily defeated Zabo's teammates.

True Loyalty
"We founded S.H.I.E.L.D. ... the real S.H.I.E.L.D. ... on the belief that leadership should operate with transparency and not from the shadows." "Nick Fury simply kept too many secrets."

- Robert Gonzales and Anne Weaver

Mackenzie brought Hunter onboard the Iliad, revealing that his loyalty lies with "the real S.H.I.E.L.D." Hunter was then introduced to Robert Gonzales and the rest of the leadership of his S.H.I.E.L.D. faction. Gonzales explained to Hunter that they saw Coulson and his erratic behavior as a threat that needs to be neutralized, and tried to convince Hunter to join them.

In the meantime, Coulson decided to pull Skye from active duty. He took her to the Retreat, Nick Fury's Safe House designed to house gifted individuals. After giving Skye special gloves made by Jemma Simmons and designed to help suppress her abilities, Coulson asked her to take some time to learn to control her powers. That night on the Iliad, though Morse tried to convince him to join them, Hunter rejected Gonzales' offer and stole an escape pod, escaping from the ship. At the meeting of the leaders, Morse decided it was time to attack Coulson's S.H.I.E.L.D. before Hunter could reach the Playground. In the Playground, after the video conversation with General Glenn Talbot who informed them about Grant Ward and Agent 33 breaking into his base to free Sunil Bakshi, both Coulson and May noticed that Mackenzie was hiding something.

Attack on the Playground
"Phil Coulson has no right to call this S.H.I.E.L.D."

- Anne Weaver to Leo Fitz and Jemma Simmons

The next day, both Morse and Mazkenzie were in the Playground, still searching for the Toolbox. While Coulson confronted Mackenzie about his secret, Agent May found Morse trying to steal the Toolbox in Coulson's office. When the EMP burst through the base, both Morse and Mackenzie escaped. Morse then called Gonzales and he ordered the attack. A gas began pumping through the Playground's vents, knocking out Coulson and all of his agents, while Gonzales' men entered the base, quickly taking complete control of it. Once the base was captured and all of Coulson's agents were apprehended with the exception of Melinda May, Gonzales called for Coulson to be brought to him. Gonzales greeted Coulson and they exchanged pleasantries for a short period, until Coulson revealed that he knew exactly who Gonzales was and his history with working for S.H.I.E.L.D., even revealing that he had intended for Gonzales to join his team. Gonzales explained his own knowledge of Coulson, expressing his concerns over Coulson's recovery with the help of alien blood and Skye's new powers. Gonzales revealed that he needed Coulson to show him how to open the Toolbox. Coulson refused to open the Toolbox for Gonzales, who gave it to one of his agents to give to Anne Weaver. Suddenly, Melinda May entered the office, knocking out Gonzales and two of his agents with an I.C.E.R. Coulson then escaped from the base via the secret elevator while May stayed behind and surrendered to Gonzales' agents. Before she surrendered, May had just enough time to call Skye at the Retreat and warn her about S.H.I.E.L.D. coming for her. Just when Skye tried to leave the area around the cabin, a group of agents led by Bobbi Morse and Tomas Calderon arrived. When Skye managed to knock down one agent, Agent Calderon fired a bullet at her, and she lost control of her powers, creating a pulse that sent the attackers flying back and obliterating the nearby trees. The same eyeless man that kidnapped Skye's father a few days earlier suddenly appeared, and teleported Skye away. Later, Coulson met Hunter at the bar on a tropical beach and Hunter accepted his offer to become a full-time S.H.I.E.L.D. agent.

The Hunt Begins
"This is not about Coulson. It's not about me. It's not about anyone on this ship. It's about S.H.I.E.L.D. We cannot afford to be enemies to each other when there are new threats out there waiting for the moment we are at our weakest. A house built on shifting sand will fall. And without a strong and united foundation, S.H.I.E.L.D. will fall again."

- Robert Gonzales to Melinda May

In the Playground, Robert Gonzales and Bobbi Morse tried to convince Leo Fitz and Jemma Simmons to open Fury's Toolbox, but Fitz openly refused. Since Gonzales was still following S.H.I.E.L.D.'s rules, he agreed to let Fitz go undisturbed. However, that wasn't true for Melinda May, who was locked in Vault D. When Gonzales visited May, he tried to convince her into seeing things his way about the enhanced persons and Coulson, but May told him that S.H.I.E.L.D. should be hunting HYDRA, and not wasting time on a witch hunt. Meanwhile, Coulson and Hunter arrived at the Retreat in a stolen jeep. Watching the security footage, they saw what Skye did the night before. The next morning, Coulson deliberetly activated the silent alarm, which was immediately noticed by Gonzales and Morse in the Playground. Using the holograms inside the cabin, Coulson and Hunter managed to distract Gonzales' men long enough to knock down two of them and steal their uniforms. However, they were eventually captured and brought into one of the agents' two Quinjets. Michael Peterson then suddenly entered the quinjet, liberating Coulson and Hunter and knocking down all the agents inside. He also prevented the other quinjet from flying off. Hearing the news about the failure of his men, Gonzales decided to try another tactic with Agent May. She was taken on the Iliad and Gonzales offered her a seat on his board, saying that Coulson should need someone who would defend him once he's captured. He also gave her a gun to shoot him if she thought of him as a traitor to S.H.I.E.L.D. May gave him the gun back, not believing that the weapon was loaded, but Gonzales showed her that it was. Later, despite Mack's attempts to get him to stay, Fitz left the Playground. When he entered the taxi and looked through his bag, he found the Toolbox, which was hidden inside by Jemma when she made a copy to deceive Gonzales' men. Agent May eventually accepted Gonzales' offer and asked to take command of the Playground base, which was granted. Anne Weaver gave her their file on Coulson and what they called Theta Protocol. Back in the Playground, with Simmons' help, May found evidences that Coulson was operating a large number of shell corporations and burning through money. Mackenzie explained that Coulson was probably building another base for powered individuals. May then ordered Simmons to open the Toolbox, unaware that the object in Simmons' possession was a replica. Meanwhile, followed by Gonzales' men, Leo Fitz ended up stuck in the restroom in a bar. Using the Toolbox, he managed to contact Coulson and Hunter, who assured him everything would end just fine.

The Deal with the Devil
"Desperate times, desperate measures. Count me in." "I'm relieved to hear you say that. We're making a deal with Ward."

- Leo Fitz and Phil Coulson

After picking up Leo Fitz, Coulson, Hunter, and Peterson traveled to Tijuana, Mexico, to find Grant Ward. They managed to capture Agent 33, forcing Ward to have a talk with Coulson. Coulson and Ward then made a deal, Ward would help Coulson stop Strucker and List in their experiments on the enhanced people, and Coulson would let Ward got free, after he goes through the T.A.H.I.T.I. protocol to wipe his memory clean. Coulson and Ward then organized a meeting between the brainwashed Sunil Bakshi and List. Peterson went with Bakshi to List's plane, playing his bodyguard. On the meeting, Bakshi offered Peterson to List, saying that he could become a great asset to HYDRA. While flying to Baron von Strucker's European base, List's plane made a stop in San Francisco. List explained to Bakshi that he was following "quantum entanglements" that could come from an enhanced individual, a teleporter.

Coulson and his team followed List and Bakshi, entering the abandoned building where they were confronted by several HYDRA agents. Though they managed to kill some of them, Hunter was wounded, and Bakshi apparently broke out of Ward's mental control, ordering his men to fire on Peterson, who managed to knock out an unknown man. When Coulson encountered Skye and her father, the teleporter appeared and took Skye and her father away. Some time later, Bobbi Morse and Alphonso Mackenzie came to the building and Coulson showed himself to them, asking them to take him to their boss, Robert Gonzales.

Reunification
"We have a chance to hit HYDRA hard. They're operating on powered people. We can shut that down and save lives." "Perhaps, but I'm gonna ask again - why should I trust you?" "Because we all have our secrets. You have one sitting in the cargo hold of your ship, but I'm still willing to work with you."

- Phil Coulson and Robert Gonzales

Coulson was brought to the Playground, and he and Robert Gonzales had a discussion on the Bus. Coulson informed Gonzales about the HYDRA facility in the Arctic that should be taken down. Though Gonzales didn't trust Coulson at first, they agreed to work together to save the enhanced people that HYDRA was experimenting on. Temporarily reassembled, Coulson's Team would infiltrate the facility and once the prisoners were rescued, Gonzales' men would bombard the place, destroying it. When the Bus approached the facility, HYDRA's missiles destroyed it, but the team safely landed in a cloaked Quinjet. When they entered the base, they quickly disposed of most of HYDRA soldiers, mostly thanks to Sunil Bakshi, who was actually still under Ward's mental control. During the battle, Jemma Simmons tried to kill Ward, but Bakshi died instead. HYDRA's leader Dr. List managed to escape, but Mike Peterson and Lincoln Campbell were rescued and brought to the Playground, though Ward preferred to stay free and leave Agent 33 in the base.

After the battle, Coulson gave Gonzales the Toolbox, only to inform him that a very much alive Nick Fury would probably want it back soon. Coulson then called Maria Hill and gave her intel gathered in List's base, including the info on Loki's scepter and its position.

Battle of Sokovia
"This is S.H.I.E.L.D.?" "This is what S.H.I.E.L.D. is supposed to be."

- Pietro Maximoff and Steve Rogers

Thanks to Coulson's men keeping the Helicarrier No. 64 safe and hidden through Theta Protocol, the former director Nick Fury, Maria Hill and a group of S.H.I.E.L.D. agents were able to use the Helicarrier and assist the Avengers when the genocidal robot Ultron attempted to eradicate humanity by turning the Sokovian capitol Novi Grad into a meteor. During the battle, Fury and his men were able to save the inhabitants of Novi Grad before the flying city was destroyed.

One S.H.I.E.L.D.
"What are you suggesting?" "One S.H.I.E.L.D., where I operate as director, under your advisement. This way, we'll have a cool underground base and a boat."

- Robert Gonzales and Phil Coulson

After the Battle of Sokovia, Coulson and the leadership of Gonzales' S.H.I.E.L.D. faction were on the Iliad, where they discussed the recent events. Coulson then proposed that he and Gonzales join forces to build one S.H.I.E.L.D., with Coulson as director and Gonzales and his council as his advisors. Gonzales and his men eventually agreed, thus ending the conflict between the two factions.

Finding a Solution
"What's our plan of attack?" "Who said anything about an attack?" "These people are a threat." "We don't know that. We don't know anything about them."

- Robert Gonzales and Phil Coulson

Suddenly, the mysterious teleporter and Raina appeared on the Iliad, and Lance Hunter set off the alarm. Phil Coulson and Gonzales saw Raina and Gordon through the security cameras, and Gonzales realized that they were looking for their special cargo. Just as the teleporter and Raina discovered the location of the cargo, Melinda May and Bobbi Morse found them, forcing them to teleport back to their base. Later, at the Playground, Gonzales' people successfully found Afterlife. Robert Gonzales called for them to prepare for an attack, but Coulson convinced him that instead they should have a meeting with the Inhuman leader Jiaying and try and resolve the matter peacefully. The first move they chose to perform was sending Skye and Lincoln Campbell back to the Inhumans' base, so they could inform Jiaying about the arrival of S.H.I.E.L.D. The two were teleported by Gordon back to Afterlife, and Skye convinced Jiaying to speak with Coulson. Back to the Playground, the council changed the plan by choosing Gonzales as the representative of S.H.I.E.L.D., using the creation of Ultron by Tony Stark as an argument to this decision. Coulson agreed to stay in the Playground.

Ambush in Afterlife
"Skye's mother orchestrated the whole thing. It was a performance."

- Phil Coulson to Melinda May and Jemma Simmons

As several S.H.E.I.L.D. agents, including Gonzales, Anne Weaver, Melinda May and Jemma Simmons, used Quinjets to fly to Afterlife, Alphonso Mackenzie announced to Coulson about his resignation and Bobbi Morse was kidnapped by Agent 33 and Grant Ward. In the Inhumans' base, Gonzales went to Jiaying's room where he found her with Skye and Calvin Zabo. Jiaying delivered to Gonzales Zabo as a first salvo towards peace. As Skye left the room so the ambassadors could talk, Gonzales explained to Jiaying that their only goal was to protect the population from powered individuals, so he asked her to put her people in the Index in case one of them would try to harm the public. Jiaying showed him a crystal but she used it to release a mist that killed Gonzales. S.H.I.E.L.D. agents and Inhumans heard gunfire from the room and saw Jiayng walking bleeding from it, claiming that Gonzales had tried to kill her.

Simmons then informed Coulson and Weaver about the scenario and the announcement of Gonzales' death was spread. Although there were divided opinions whether Gonzales had shot or not, Coulson agreed that the security of the agents was the important part. But new problems were emerged, as a single Quintet fired two missiles at a house, what made Skye and the other Inhumans to believe that S.H.I.E.L.D. wanted to start a war.

Pressing Matters
"They just want to live in peace. Is that such a crime?" " Your wife assassinated a high-ranking S.H.I.E.L.D. officer, then staged it to look like we attacked them. Wake up, Cal. She's trying to start a war, and your daughter's gonna be caught in the middle of it."

- Calvin Zabo and Phil Coulson

Meanwhile, Bobbi Morse was tortured by Grant Ward and Agent 33 in order to make her regret of extradite Agent 33's safe house location while she was hiding there, during Morse's time as an undercover HYDRA agent. This action caused Agent 33 be brainwashed. Morse didn't show any regret, so Ward tied Morse back to a chair and rigged a rifle behind her. Ward explained that he would make her to watch as someone else was killed while attempting to save her. He told her that the rifle was set to fire at the doorway when someone opened it, killing them instantly in front of her eyes. In the Playground, Coulson discovered that Jiaying killed Gonzales and orchestrated the attack of S.H.I.E.L.D. on the Afterlife. Lance Hunter and Leo Fitz then located Morse's location and Hunter and May flew to there to save her. While Calvin Zabo was locked up in Vault D, Coulson presented him all the facts that Jiaying wanted to start a war and she was using him, just like when she used him to kill all the people in the village in Hunan province. Coulson also said that she had probably ordered him to take his formula that was killing him. Zabo said that he took it so he could have the power to kill every agent he can. Coulson continued to argue with Zabo about the true nature of Jiaying, until Zabo got a heart attack. Zabo was brought to the lab, where Jemma Simmons injected adrenaline. The material transformed him to a powerful monster. Coulson wanted to talk in reason with him, so Simmons and Fitz led him to the hangar where Coulson captured him and started talking with him.

During that time, a group of Inhumans led by Gordon took control on the Iliad, killed and captured most of the agents on the ship. Only Alphonso Mackenzie was left to fight them. Anne Weaver sent to Coulson a message and asked for his help. After the hijack succeed, Jiaying was welcome aboard and said that they will start the next step.

Hijacking and Retaking of the Iliad
"We'll need every asset we've got to shut these Inhumans down."

- Phil Coulson

Eventually, Coulson and Zabo agreed they should work together to save Skye from Jiaying. Meanwhile, Mackenzie freed Skye from her cell in the Iliad, and asked for her hacking skills. In the Command Room of the ship, Jiaying ordered her men to take a case of Terrigen Crystals to the ventilation room and the rest to the Quinjet. Lincoln Campbell then entered, saying that a emergency beacon had been sent to Coulson's base. Jiaying asked Anne Weaver and Oliver if they could expand the beacon. The two refused, and Jiaying used a Crystal to kill Oliver. Once she saw Oliver, Weaver agreed to do her bidding. Skye and Mackenzie watched the event and realized that Jiaying's plan was to kill every S.H.I.E.L.D. agent who was on the ship, making a plan to cut off the beacon. In the Playground, where Zabo was stabilized, Leo Fitz informed Coulson that the emergency beacon from the ship came. Coulson said to him that they would need every available agent they had to shut the Inhumans down. Meanwhile, Melinda May, Lance Hunter and their team entered an abandoned warehouse, where Bobbi Morse was being held by Grant Ward and Agent 33. Hunter found Morse bleeding after she saved him from a rigged rifle shot. May tricked Ward and used him to kill Agent 33. They then flew to the Playground to save Morse's life.

Fitz then informed Coulson he had created a device that could make Gordon stay in a single location and not teleport. Coulson told him that there were Quinjets all over the world which flew to answer with them to the emergency beacon. May and Hunter returned with Morse to the base and Simmons started to operate on her.

When the squadron of Quinjets flew to the Iliad, Coulson, May, Fitz and Zabo, who were in the lead Quinjet, received a message from Skye, saying that they were entering a trap. Coulson then ordered the other Quinjets to fall back, but his Quinjet continued with the plan.

As they landed on the ship, they received another message from Skye, warning them of the Terrgin Crystals. Zabo then realized Jiaying's plan and explained it to them. Despite the risks, the S.H.I.E.L.D. team went to free the ship. Mackenzie protected the Crystals in the ventilation room while Gordon attempted to reach them. Meanwhile, Skye fought Alisha and her duplicates. Though Alisha almost overpowered Skye, May and Lincoln helped her and defeated Alisha. Coulson and Fitz then joined Mackenzie in his battle, with Fitz placing the device that would hinder Gordon. The device kept Gordon in the room, and he teleported onto a pole Fitz was holding, impaling himself. However, as he died, he dropped a Crystal with Coulson instinctively caught. As his arm petrified, Mackenzie used his axe to cut it off. Skye then found her mother entering the Terrigen Crystal-laden Quinjet to finish her plan of dropping the Crystals and killing non-Inhumans. The two women fought each other, each using her powers to overcome the other. Skye gathered one burst of energy and blasted the Quinjet into the ocean, ruining Jiaying's plan. As Jiaying tried to kill her daughter, Zabo appeared and broke the two apart, killing Jiaying to spare Skye the pain of killing her own mother. The human race was saved and the Inhuman threat was no more.

New Order
"We have to do this. We don't have a choice. It may feel like things have cooled down right now, but this... this is my permanent reminder that we'll always be paying the price, that we'll never get ahead of the consequences that I, that you, that S.H.I.E.L.D. have set in motion."

- Phil Coulson to Skye

With the Inhuman threat eliminated, Phil Coulson returned to work and began planning out new ways of dealing with threats against the earth, employing his S.H.I.E.L.D. agents into new positions which best supported their views. He brought Andrew Garner back to assess his team and judge their readiness to continue working in the field. They discussed having Alphonso Mackenzie back on the team in charge of all alien dealings before Coulson teased Garner about getting back together with Melinda May, who took time of as an agent. Garner then handed Coulson a file of his recommendation for Coulson's new program.

Coulson put the order in for Calvin Zabo to go through the T.A.H.I.T.I. Program, allowing him to begin a new, peaceful life as a vet named Dr. Winslow. Coulson joined Skye as she went to visit Zabo at his new office before asking Skye about her thoughts on leading a new team for people with powers, where they could use their abilities to help protect the world. Skye insisted that if they did this, the team should be kept a secret so the people involved could still live their own private lives. Coulson agreed, noting that his missing arm would be his personal reminder of S.H.I.E.L.D.'s past mistakes. Bobbi Morse recovered from the operation and talked with Lance Hunter, saying she could not do it anymore.

Jemma Simmons later was swallowed by the Monolith.

New Missions
"The rate of new cases is increasing." "We knew it would after the initial reports." "A new Inhuman could emerge anywhere without having any idea what's happened." "Only in the continental U.S. so far."

- Daisy Johnson and Phil Coulson

A few months later, S.H.I.E.L.D. had to deal with a new threat: the new Inhumans that were created by the Nature Max Supplements Fish Oil pills that had the Terrigen Crystals material inside it. S.H.I.E.L.D. tracked the fish oil pills and managed to get them off the market as soon as they discovered they had been manufactured from an area contaminated by Terrigen Mist. However, they were unable to track down the pills that were already bought, and at least five individuals managed to take them before S.H.I.E.L.D. could locate them. S.H.I.E.L.D. thought that the new Advanced Threat Containment Unit was responsible for the capture and the deaths of those Inhumans. Phil Coulson appointed Skye, who now was going with her birth name Daisy Johnson, and Alphonso Mackenzie to track the Inhumans and get to them before the mysterious organization could with the help of their new plane, Zephyr One. They also tracked HYDRA financing activities, but no HYDRA member did such action.

At the same time, S.H.I.E.L.D. had already discovered that Jemma Simmons had been swallowed by the Monolith and was now probably dead. However, Leo Fitz refused to believe that and he went on a search across the world to prove Simmons was still alive. While Fitz went to different locations in the world, Bobbi Morse covered his assignments in the Playground. Lance Hunter was planning revenge on Grant Ward for what he had done to Morse. He was sure that Ward returned to HYDRA in order to rebuild it and fight against S.H.I.E.L.D.

First Encounters
"My name's Daisy and I'm with S.H.I.E.L.D. and we're here for your protection."

- Daisy Johnson to Joey Gutierrez

Joey Gutierrez was the sixth person who went through Terrigenesis because of the Nature Max Supplements Fish Oil pills. He possessed the power of melting every metal. The Advanced Threat Containment Unit quickly showed up to arrest him but he managed to escape them. Daisy Johnson, Alphonso Mackenzie and Lance Hunter came to rescue him from the soldiers and succeeded to bring Gutierrez to Zephyr One safely. After the fight, Phil Coulson took a picture of who he assumed was the leader of the unit.

In the Playground, Johnson explained to Gutierrez what had happened to him and that his life could not be normal anymore. Coulson discovered that the woman he pictured had many identities and worked for many agencies.

Meanwhile, Leo Fitz went to Morocco to retrieve an old parchment that describe exactly what the Monolith was so he could know how to save Jemma Simmons. He tricked Yusef Hadad to give him the parchment and he then returned to the base. Johnson and Mackenzie went to see Lincoln Campbell to ask him to help Gutierrez adapt to the change he had experienced. Coulson and Hunter went to meet the leader of the Advanced Threat Containment Unit in a subway train but entered into an ambush. Rosalind Price revealed to Coulson that she knew that she had been killed and came back to life in Project T.A.H.I.T.I. She also thought that S.H.I.E.L.D. had killed all the Inhumans with an energy weapon, but Coulson said that he thought it was her who killed them. She asked him then who had killed them. Coulson and Hunter managed to escape the train with a Containment Module from Zephyr One. In the hospital where Campbell worked, Johnson asked for his help, but he refused, saying that being Inhuman was a curse and he just wanted have normal life. To the hospital came an monstrous man who was looking for Campbell. The three fought against him. He ultimately escaped and the three as well after the ATCU came.

As all the S.H.I.E.L.D. agents watched President Matthew Ellis' press conference as he revealed that he ordered the foundation of the ATCU, Fitz translated the words on the parchment to "Death". Coulson said to him to accept the death of Simmons.

Saving Simmons
"No. No, I'm proving that it's a portal, okay, to another planet, a-a very old planet, a crack in space-time that carried Simmons away and carried the sand back. Which means-" "She's out there. But it's been months."

- Leo Fitz and Phil Coulson

After Coulson, Johnson, Mackenzie, Morse and Hunter polled out Fitz from the Monolith's containment, Fitz found on Morse's finger sand grains. He explained that the Monolith was a portal to another world and Jemma Simmons must be there. Coulson asked for Elliot Randolph's help to understand the Monolith, while Johnson and Mack helped Andrew Garner's assessment on Joey Gutierrez and Hunter went to his revenge camping against Grant Ward and he also recruited Melinda May for the mission. Randolph led them to a room in an English castle where the Monolith could be opened and become a portal. Mackenzie and Johnson brought the Monolith and after Fitz activated the machines of the room, the Monolith changed to his liquid form, but the machines broke and it changed back to solid. But Fitz had an idea that they could use Johnson power to change the Monolith to a portal. Johnson indeed opened it and Fitz jumped through it to search for Simmons, and so he did. Simmons was brought to Earth and the Monolith was exploded.

Cooperation with the ATCU
"So... so now we're working with them?" "I'm done fighting with people over who gets to fight the real fight. It's a colossal waste of time and resources. I went against Talbot. I went against another faction of S.H.I.E.L.D. We know what we're doing, they don't. Hopefully, they can learn from us."

- Daisy Johnson and Phil Coulson

With the Advanced Threat Containment Unit continued hunting Lincoln Campbell, Phil Coulson ordered Daisy Johnson to find him. Campbell called for her for help and Johnson and Alphonso Mackenzie went to his location. Coulson arranged a meeting with Rosalind Price and the two met. Coulson, knowing she had a picture of Johnson, agreed to let the ATCU take Campbell. However, Campbell escaped, so Luther Banks ordered his soldiers to arrest Johnson. Coulson offered an alliance between S.H.I.E.L.D. and the ATCU. Pierce agreed and ordered her men to leave the place. A recruit mission for the Caterpillars program was interrupted by the monstrous man. The ATCU helped S.H.I.E.L.D. to hunt him. Johnson suspected Dwight Frye that he might be the Inhuamn killer, and shred the information with the ATCU. Outside Frye's house, Coulson, Johnson and Alphonso Mackenzie met Rosalind Price and Luther Banks. They entered the house together and found Frye hiding. He told them that the killer was called Lash, and he gave him the Inhumans' names Lash wanted to kill. When the ATCU drove with Johnson and Mackenzie to their base to put Frye in custody, Lash broke in the truck and killed Frye. Johnson managed to see him transform into a human. Meanwhile, Lance Hunter managed to get high enough in the ranks of HYDRA to meet Grant Ward. Melinda May was afraid that he will fail and possibly be killed if he storms alone against Ward. May went to the Playground and asked Coulson for backup. Hunter and May fought against Ward and his men. Ward ordered Werner von Strucker to get close to Andrew Garner in order to make May and Hunter surrender. May asked Coulson, who was on his way to help them, to save Garner. One of Coulson's men guarded Garner, but he was killed by one of Ward's men. Hunter refused to let Ward escape and shot him but only hurt him. Ward managed to escape alive. As a result, May thought that Garner was probably dead, but he survived the explosion of the shop that was caused by HYDRA. S.H.E.L.D. brought the wounded Garner to the Playground. May recruited Bobbi Morse to kill Ward. They followed Werner von Strucker in order to find him so he would lead them to Ward. They tracked von Strucker's location in Lisbon, Portugal. They entered his home, only to find him being tortured by Kebo. A fight brook between May and Morse to Kebo and his man. Morse managed to kill Kebo and May tried t questioning von Strucker, but he went into a coma. Meanwhile, Coulson was invited by Price to the ATCU Endotex Labs. After Johnson explained to him why she thought Luther Banks might be Lash, Coulson ordered her to follow him. Johnson, Mackenzie and Hunter kidnapped him and took a blood sample from him and sent it to Jemma Simmons, to conform that he was an Inhuman. Simmons conformed he was not. Then, they arrived to the Labs where Banks was scheduled to arrive and sent a D.W.A.R.F. inside. They found Price and Coulson there with a composed and imprisoned Inhuman. The three were appalled, but noticed that Coulson did not seem to have the same reaction.

Lash's Identity
"Lincoln gave me names. I checked them against the bodies we could identify." "That's how I knew Lash was using Jiaying's ledger to find us." "Her ledger?" "She kept a genealogy of Inhumans. She was the only one allowed to use it, until..." "Until S.H.I.E.L.D. recovered it. And there's only one person I know who had access." "Dr. Garner? But there's no way. It's not possible."

- Alphonso Mackenzie, Lincoln Campbell, Daisy Johnson and Phil Coulson

Phil Coulson, Daisy Johnson and Andrew Garner argued about the cure the ATCU tried to develop for the Inhumans. Coulson then told them that he and Rosalind Price would meet with president Matthew Ellis and discuss about the Inhumans issue. Garner went to the Cocoon for Joey Gutierrez's evaluation, when suddenly Melinda May interrupted and demanded Garner to talk with her. Price came on Zephyr One and so Alphonso Mackenzie and Lincoln Campbell, who explained that Garner might be Lash. Coulson, after he had learned the Garner and May were missing, changed direction to find them. Campbell explained that Garner was in period of transition to become Lash forever. S.H.I.E.L.D. found them in an abandoned building in Culver University. Coulson saw her shackled in a tank. Coulson and Garner were talking about Lash's actions, when Campbell entered the room. Garner turned into Lash and Campbell attacked him. May freed herself while Lash attacked everyone he came across with. May stopped him and talked with him and as he turned back to Garner, she shot him and he felt right into the Containment Module.

After the battle, Campbell joined S.H.I.E.L.D. and Garner was hold in the Module in his human form to prevent him becoming Lash.

Operation Spotlight
"Today, we're launching Operation Spotlight. The objective... to peer into every shadowy corner of the ATCU."

- Phil Coulson

As the ATCU took Andrew Garner in the Containment Module to the Endotex Labs to find a cure for him, Phil Coulson invited Rosalind Price to the Playground so they can discuss this situation. In the base, Coulson summoned his agents and explained Operation Spotlight, an undercover mission in witch S.H.I.E.L.D. would infiltrate the ATCU base and reveal their secrets. Bobbi Morse and Lance Hunter managed to infiltrate the base. Morse came to a classified area, where she discovered that the ATCU did not try to find a cure, but instead they tried to turn every person they could into and Inhuman. Coulson got the information and interrogated Price if she was an HYDRA operator. Price said that the updates she reserved from that section came from Gideon Malick, who Price suspected might be in HYDRA. She called Luther Banks and ordered him to escort Morse and Hunter, who had fought the Inhuman Giyera, until Melinda May would take them back to the base.

Afterwards, Jemma Simmons and Leo Fitz, who were working on a way to go back to Maveth and save Will Daniels, who had been in the planet at same time Simmons was, explained to the team that HYDRA was actually an ancient organization who supported a project of delegations to Maveth.

Hunting Ward
"Here's the deal. What HYDRA's planning is gonna hurt a lot of innocent people, maybe people you care about. I wouldn't be asking you for your help if I didn't think we had a chance. So either you step up and do the damn job or you let the bad guys win. The choice is yours."

- Alphonso Mackenzie to Joey Gutierrez and Lincoln Campbell

When Phil Coulson and Rosalind Price had a dinner in her place, she was assassinated by Grant Ward. Ward sent after him assassins and Coulson fought them and escaped with the assistance of Alphonso Mackenzie. At the Playground, Coulson interrogated each member of his original team in an attempt to find anything about Ward he could use against him. Before he went to find Ward with the help of Bobbi Morse and Lance Hunter, he had appointed Mackenzie to be the acting Director of S.H.I.E.L.D. until he would return. He also sent Jemma Simmons and Leo Fitz, alongside Luther Banks, to an abandoned Project Distant Star Return facility, but they were ambushed by Giyera, who killed Banks and kidnapped Fitz and Simmons. Mackenzie got the information about Fitz and Simmons kidnapping and sent it to Coulson. Coulson, knowing that he could not fail, raided with Hunter a bank and kidnapped Ward's brother, Thomas. He called Ward and let him talk with his brother until they traced the call and found his location in the HYDRA Castle. Meanwhile, Mackenzie also found HYDRA's location and asked Melinda May for advice since the Castle was heavily fortified and he believed Coulson was on a suicide run; May advised him to be a leader. Mackenzie green-lighted the Caterpillars project and made Joey Gutierrez and Lincoln Campbell official agents and Daisy Johnson as their leader, as all prepared for an Attack on the HYDRA Castle. Coulson saw Ward, through the heat signal, entering the portal to Maveth with Fitz or Simmons with him, so he jumped from the Quinjet straight through it and landed on the planet.

Attack on the HYDRA Castle
"Okay. So, are we rescuing Inhumans or saving Coulson or attacking HYDRA or is there some kind of combo? Sorry. New guy just trying to understand how this whole S.H.I.E.L.D. thing works." "This is how S.H.I.E.L.D. works. You make a plan, plan turns to rubbish, we make a new plan."

- Joey Gutierrez and Lance Hunter

Bobbi Morse and Lance Hunter landed on Zephyr One and told Alphonso Mackenzie why Phil Coulson had jumped to the portal.Daisy Johnson informed the team that HYDRA had brought dozen contained Inhumans to the castle. Mackenzie came with plan: he said that one team would predominant the portal chamber while another team would search for Leo Fitz or Jemma Simmons. Johnson located an aqueduct that led straight to the castle. Once the team reached the aqueduct, Mackenzie, Morse and Hunter went to predominant the chamber while the Secret Warriors and Melinda May went to search for Fitz and Simmons. The two teams succeeded in their tasks and they reunited in the portal chamber. As they discussed what to do next, they noticed that May was missing, so Simmons explained that Andrew Garner was in the castle and had saved her life, so May probably searched for him. She also told them that Gideon Malick wanted to bring back from Maveth the ancient HYDRA leader, so he had sent Fitz and Grant Ward to find him. the Inhumans in the castle were meant to serve him as an army. May entered the chamber and informed that all of the Inhumans were killed by Garner. As the HYDRA soldiers were getting closer to the chamber, Mackenzie ordered his agents to go back to Zephyr One and blow the castle in case the HYDRA leader would return to Earth. Only he and Johnson staid and waited for Coulson and Fitz to return, while the rest returned to Zephyr One and waited for Mackenzie's orders. Then, Mackenzie ordered May to blow the castle, as he and Johnson returned to the plane inside the Containment Module, along with Fitz and Coulson, who had killed Ward on Maveth.

Meeting President Matthew Ellis
"The image of Helicarriers crashing down on the nation's capital is hard to forget." "Then why is this meeting happening if S.H.I.E.L.D. doesn't exist?" "Because I need you to keep doing what you're doing. Privately. Publicly, the ATCU will still be the face of my administration's response to advanced threats."

- Matthew Ellis and Phil Coulson

President Matthew Ellis and Phil Coulson met together in residence of the recently deceased Rosalind Price. President Ellis recognized that he needed S.H.I.E.L.D. to help deal with the alien threat, but he couldn't bring S.H.I.E.L.D. out of the shadows just yet, as the public still remembered what happened in Washington, D.C.. However, the President and Coulson arranged for S.H.I.E.L.D. to take point on containing the alien threat while the ATCU would act as a supporting organization. Coulson wanted to find Gideon Malick, so he used the Theta Brain-Wave Frequency Machine on Werner von Strucker and discovered a location where he could communicate with him. He went there and called him, saying to Malick that he was after him. However, Malick was not so threatened by Coulson.

Meanwhile, in Bogotá, Colombia, S.H.I.E.L.D. tracked the new Inhuman, Elena Rodriguez, who possessed super-speed ability. After they understood Rodriguez used her ability to get rid of the weapons in the city, Daisy Johnson, Alphonso Mackenzie, Bobbi Morse, Lance Hunter and Joey Gutierrez assisted her to destroy the National Police of Colombia's gear of weapons. After the battle, Johnson and Mackenzie agreed they should join Rodriguez to the Secret Warriors.

Symposium on Alien Contagion
"We need to know if any of these countries are harboring Inhumans." "So it's a sneaky, little spy mission." "S.H.I.E.L.D., remember? That's how we roll."

- Phil Coulson and Glenn Talbot

Phil Coulson was informed by Matthew Ellis that Glenn Talbot was the new head of the ATCU. The two met and discussed the Symposium on Alien Contagion. Despite his agents' resistance, Coulson agreed that Talbot's bodyguard, Carl Creel, would join in their mission, to discover who of the symposium' delegates was Gideon Malick's inside man. While Coulson and Talbot were in the meeting, May, Morse and Hunter searched in the delegates' rooms for clues. Hunter discovered that Talbot's son was inside Suspension Gel. Malick entered the meeting room and accused Coulson to be HYDRA's director. Coulson discovered that Talbot was Malick's inside man due to blackmail on his son's life. He ordered his men to kill Coulson and Talbot, but, with the help of Creel, they escaped. Morse and Hunter penetrated Malick's plane.

Spy's Goodbye
"We took an oath to be the shield." "To protect those in danger." "Well, now S.H.I.E.L.D., this team, is in the cross hairs. And the right thing for us to do is take the bullet."

- Bobbi Morse and Lance Hunter to Phil Coulson

Bobbi Morse and Lance Hunter arrived in Siberia and the rest of the team followed them. Morse infiltrated the meeting between Gideon Malick and Russian leaders, discussing the Inhumans and the proposed sanctuary for them. The team learned that the Russian minister of defense, General Androvich, was an Inhuman, and Phil Coulson realized that Malick planned to use the minister to stage a coup and kill the prime minister of Russia. Coulson ordered his team on the ground to rescue the prime minister. To do so, Morse killed Androvich but was captured along with Hunter. The two did not tell that they were S.H.I.E.L.D. agents during their interrogation. With the help of President Matthew Ellis, Coulson was granted permission to speak with Morse and Hunter. As Coulson explained his plan of escape, the two refused to run, stating that to keep S.H.I.E.L.D. a secret, they would allow themselves to be disowned. Coulson and his team said their goodbyes to them at a bar.

Watchdogs
"They gave up their right to civil liberties when they started imploding buildings." "Maybe, but it's not about how they act. It's about how we respond."

- Daisy Johnson and Alphonso Mackenzie

After the Watchdogs destroyed the headquarters of the ATCU, Phil Coulson found out that the leader of the group was the former S.H.I.E.L.D. agent, Felix Blake. To test Lincoln Campbell's loyalty to S.H.I.E.L.D., Coulson went with him to one of Blake's safe houses, where they met him. Blake told them his aversion, with the Inhumans, so Coulson ordered Campbell to kill him. Despite his disagreement, Campbell fired a blast of electricity at Blake only to learn it was merely a hologram. Cooulson was satisfied with Campbell.

Meanwhile, Daisy Johnson found the operations base of the Watchdogs. There, the Watchdogs mistaken Alphonso Mackenzie to be an Inhuman, and went to kill him. Mackenzie and his brother dealt with them, with Mackenzie suffering with a moderate injury.

Later, Johnson told Coulson that Gideon Malick secretly supported the Watchdogs with weaponry.

Fighting the Future
"Wish we could practice every moment of our life like this."

- Phil Coulson

S.H.I.E.L.D. traced an emergency call of Edwin Abbott, who asked for Daisy Johnson's help against HYDRA. She met him and he told her the Inhuman, Charles Hinton, had made him see the future and his death by HYDRA. And indeed, an HYDRA QuadCopter arrived, killed Abbott and escaped with Hinton.

At the Playground, Johnson told the team about a vision she had seen as she had tried to rescue Hinton. She told about a fight she would do to save Hinton. Phil Coulson suggested to let Melinda May go to save him instead since Johnson had not seen her in her vision. Johnson trained May for the battle. They found the building where Hinton was held was owned by Transia Corporation. May was ready to go there but suddenly, Andrew Garner entered the base and told her he was soon to permanently be Lash. As May stayed in the base with Garner, Johnson replaced her. Leo Fitz was able to hack the security cameras of the building. To the team's surprise, Grant Ward was shown before the transmission was cut off. Fitz said that he feared he was Hive. Coulson and Lincoln Campbell entered the building to find him. Johnson fought the HYDRA guards and was saved by Coulson. He ordered her to go to the roof where Hinton was held. Campbell saw Ward but Coulson ordered him not to attack him. Johnson arrived at the roof, where Gideon Malick waited for her. The two had a duel and with Hinton's help, Johnson defeated Malick but Hinton was killed by him.

Hijacking and Retaking of Zephyr One
"Everyone from our team is on that plane." "Not everyone. You put together the Secret Warriors Initiative for a reason." "No, Lincoln, what-what if..." "You can't be afraid of that vision. We both know we got to do something." "Let's call them in."

- Daisy Johnson and Lincoln Campbell

With the acknowledgement that Hive had returned to Earth inside Grant Ward's corpse, Phil Coulson briefed his agents about their next move against him. He told them that after Gideon Malick had taken over Transia Corporation, HYDRA raided its subsidiary GT Agrochemical and confiscated equipment. While riding Zephyr One, they received a footage of Giyera inside the facility, so they planned to kidnap him. Coulson, Melinda May and Alphonso Mackenzie entered the facility and saw the destroyed research. Makcenzie discovered the facility's data had been transferred. Giyera discovered them and after a brief fight with May, she knocked him out and they brought him to the Containment Module in Zephyr One.

Leo Fitz found that the data had been transferred to Schoonebeek Oil Field. Jemma Simmons told Coulson that Hive was maybe afraid of the the research so he had ordered its destruction. They realized that Hive was a parasite that could consume human skin and keep the memories of the bodies he took over. Suddenly, Giyera managed to escape the Module and took control of the plane and landed it in the oil field. May called Daisy Johnson for help. Johnson and Lincoln Campbell knew they had to reassemble the Secret Warriors in order to save their friends. Daisy Johnson and Lincoln Campbell recruited Joey Gutierrez and Elena Rodriguez on their way to save the agents locked in Gideon Malick's base. Once the Secret Warriors reunited, Johnson led her team to an attack on the base. Meanwhile, Phil Coulson, Melinda May, Jemma Simmons, Leo Fitz and Alphonso Mackenzie locked themselves inside a room in Zephyr One and prepared to strike HYDRA back. Using their powers, Johnson opened the hangar's hatch, Campbell caught Malick, Rodriguez rescued the rest of the team and Gutierrez killed Lucio. With Zephyr One being retaken, the team escaped from the base back to the Playground.

Fallen Agent
"Hive can sway Inhumans. Your team may have been exposed in the rescue." "Wait. Sway. Like mind control?" "One of you killed Malick. I'm trying to keep everyone safe, including you."

- Phil Coulson and Lincoln Campbell

At the Playground, Phil Coulson interrogated Gideon Malick, who revealed to him that Hive could control Inhumans' minds. Fearing that one of the Secret Warriors had been swayed by the dark Inhuman, Coulson ordered Alphonso Mackenzie to lock down the base. Coulson kept the information from the Inhumans and asked Leo Fitz and Jemma Simmons to find in Lucio's corpse something to prove Malick was right. The pair found an infection in Lucio's brain. Suddenly, the power in the base was turned off. S.H.I.E.L.D. agents surrounded the Secret Warriors, suspecting that one of them caused the power outage and Malick's death. The team barricaded themselves. Mackenzie found in Lincoln Campbell's locker the Kree Orb. Daisy Johnson led the team in to a room where Coulson waited for them. He accused Campbell for being under Hive's control since the their first encounter with Hive. Campbell tried to escaped but Johnson knocked him out.

As every Secret Warriors member was in isolation, Coulson said to Johnson that he disbanded her team. Later, the base started shaking, revealing that Johnson was the one who was under Hive's control. She escaped from the Playground with the Kree Orb and some Terrigen Crystals.

Search for Hive
"Daisy's still one of us. What she did here was not of her own free will. Hive infected her. She's his hostage. We need to remember that. But this alien creature messed with the wrong team. It thinks if it breaks our legs, we'll stop fighting, but it doesn't know how damn stubborn we are, especially when it comes to protecting our own. Hive is building an Inhuman army, but we're not gonna let that happen."

- Phil Coulson to his agents

As S.H.I.E.L.D. agents were repairing the base, their planed their next move: finding Daisy Johnson and cuing her. Jemma Simmons, Leo Fitz and Alphonso Mackenzie went to Bucharest to ask Holden Radcliffe's help to cure their friends, while Phil Coulson, Melinda May and Lincoln Campbell searched for Hive. Simmons, Fitz and Mackenzie encountered Hive, Johnson and Hellfire, who kidnapped Radcliffe and warned the three not to follow them. After they failed finding Hive, Coulson and May returned to the base, he showed her the attack of Glenn Talbot on all known HYDRA bases across the world given by Gideon Malick, putting end for HYDRA.

Battle of Union City
"This may be our only chance to catch Hive by surprise." "And worst-case scenario, if Hive can't be killed?" "I suggest running, very fast away."

- Phil Coulson and Alphonso Mackenzie

With the facial scan program, Phil Coulson found Daisy Johnson in Union City. Coulson explained to Alphonso Mackenzie that they were going to kill Hive. Mackenzie, Melinda May, O'Brien and Piper used Zephyr One to arrive to Union City. Upon their arrival, May seduced Hellfire to tell her where Hive was. After he told her, the team entered an abandoned facility where they saw the Kree Orb in action. Coulson on Zephyr One saw an object in space heading to their location. The object crashed and two Kree came out of what appeared to be their satellite. The team observed as the Kree killed every one they encountered. One of them fought against Hive while the other was killed by Johnson. Mackenzie tried to convince Johnson to come with him, but she refused, telling him that Hive planed to turn every human into an inhuman. Hive killed his opponent, so May and Piper tried to kill him, but he could not be killed. They ran from him, saved Mackenzie from Johnaon and escaped in the Containment Module from the scene.

Return of Agent Johnson
"It's time for S.H.I.E.L.D. to come in from the cold relegitimize." "In exchange for revealing and registering any Inhumans we may have? Not gonna happen." "Why are you so pigheaded? It's good enough for the Avengers." "Not all of them. And the Avengers operate in the spotlight. We work in the shadows."

- Glenn Talbot and Phil Coulson

Phil Coulson gave Glenn Talbot a tour in the Playground, showing him the Inhumans S.H.I.E.L.D. agents and even Lash. Talbot tried to make Coulson sign the Sokovia Accords, but he refused. Coulson, Jemma Simmons and Leo Fitz told Talbot about Hive, his control over Daisy Johnson and his plan to turn Humans into Inhumans, with them he wanted to rule the world. Lincoln Campbell managed to escape from his isolation with the help of Johnson. It seemed he managed to take a Quinjet to fly to Johnson. However, he and Melinda May revealed that they had actually put Lash inside the Quinjet, so he could kill Lash, thus saving Johnson. Johnson returned to the base on the Quinjet and told the agents that Lash had sacrificed himself to free Johnson, but he had failed to kill Hive. Simmons and Fitz explained to Coulson and Talbot that with the new information Johnson had given to them, they feared that Hive planed to release a virus that turned Humans into swayed Primitives. Talbot revealed that Hive had taken from the ATCU a warhead, capable of creating a sockwave to infect a huge amount of Humans.

Showdown against Hive
"We're two sides of the same coin, Coulson, commanders leading soldiers." "The only difference is, when you give an order, you followers have no choice but to obey. But when I gave my team the order to stay behind, they just wouldn't listen."

- Hive and Phil Coulson

Using Daisy Johnson's information, S.H.I.E.L.D. found out that Hive planed to launch his nuclear missile from an island in the Pacific to the atmosphere. Melinda May, Alphonso Mackenzie, Lincoln Campbell and Elena Rodriguez used the Quinjet to get there and to stop the launch. Phil Coulson got the government cancellation code and he delivered it to Leo Fitz, who successfully stopped the launch. May rescued Holden Radcliffe from the Primitives, however she could not stop Giyera from taking the warhead. With the dismantled Theta Brain-Wave Frequency Machine, the rest of the on the ground detained Hive to follow them as they rescued the staff of the base he had taken. As they ran to the Quinjet, Hive was about to attack them, but they put him inside the Suspension Gel. Upon arriving of the team, Coulson put the Suspension Gel in the hangar and locked down the base. As Fitz and O'Brien checked on the Suspension Gel, a blast from the amendment parts for the hangar released the Absolution Virus. O'Brien and other agents turned into Primitives. Jemma Simmons managed to get Fitz out of the hangar. The Primitives then freed Hive. Mackenzie rushed to the Coulson's office and told him that Hive knew what Zephyr One was capable of and he could use it as his new missile. Johnson brought her Containment Module to Zephyr One and dulled Hive by herself.

Meanwhile, the Primitives managed to enter the base. May and Fitz hided in Zephyr One as Hive took control on the plane and flew to the atmosphere. One of the Primitives shot Rodriguez as three turned off the power of the base. Coulson, Mackenzie, Campbell and Radcliffe locked themselves in a room, there they threaded Rodriguez wounds. They sensed that the heat increased, so Radcliffe realized Simmons had done it to blind the Primitives. They got out from the room and went to Coulson's office. At the same time, May and Fitz found Johnson inside the Containment Module. However, Giyera knocked May out and threatened to kill Fitz, but the latter used a Cloaked Gun to kill Giyera. Fitz freed Johnson. In Coulson's office, he called a Quinjet with which the team brought Rodriguez in an hospital and then flew to Zephyr One. Coulson refused that they would come with him, but they insisted to stop Hive with him. As they arrived, Coulson distracted Hive with an hologram so they could sneak into the plane. Coulson explained to his team that he would set the Quinjet to fly to outerspace with the war head inside it. They found that Johnson was missing and Campbell said she went to put the war head inside the Quinjet. Suddenly Hive and the Primitives came and the team defeated the creatures, but Hive went after Johnson. Campbell got to the Quinjet before Johnson and flew from Zephyr One to space with Hive and the war head with him, the team watched as Johnson begged Campbell to come back, but he was willing to sacrifice himself. They saw through the screen as the Quinjet exploded in space, killing Campbell and Hive. The team sorrowed the death of their colleague.

Manhunt after Quake
"As soon as Talbot gave the location of this base to the president, things changed. I knew we'd be divided, undermined, kept in the dark, so I have been clawing for as much power as I can possibly grab to keep a modicum of control over any of this. After all we've been through... I don't trust the new Director, but he trusts me, so now, in order to keep that trust, I must take the appropriate action to address this break in protocol. I'm sending you and your strike team to take Coulson and Mack out of the field, by force, if necessary."

- Jemma Simmons to Melinda May

Several months after Hive's defeat and Lincoln Campbell's sacrifice, S.H.I.E.L.D. was once again legalized and the agency accepted the Sokovia Accords. In order to keep the fact that he was alive a secret, and to help improve the standing of Inhumans, Phil Coulson resigned from his position as director of S.H.I.E.L.D. and was replaced by Jeffrey Mace, an Inhuman. Mace appointed Jemma Simmons as Special Advisor to the Director in Science and Technology, being one of his most trusted advisors. Also, as part of his moves to separate Coulson's former inner circle, Mace assigned Melinda May the task of creating, training and leading a specialist strike team. After Yo-Yo Rodriguez signed the Accords, and with the help of the team, she revenged her cousin's death on Victor Ramon. Daisy Johnson abandoned S.H.I.E.L.D. and became a vigilante known as Quake. Mace appointed Coulson and Alphonso Mackenzie to run the pursuit after her. One day, Coulson found Johnson speaking to Polly Hinton. He ordered the agents to get her, but she escaped from them. Coulson ordered to seal the perimeter, although he knew they lost her. He and Mackenzie then discussed where they would be assigned. The Director pulled them from the pursuit, convinced that Coulson was letting Johnson to escape. May got information from one of her contacts in law enforcement, that a Johnson might be in Los Angeles, as part of her fight against organized crime. Making sure Mace would not know it, May called Coulson and Mackenzie to the Playground and gave them the information. Contrary to the orders they had been given, Coulson and Mackenzie investigated Johnson's fight against the criminal organisation, Aryan Brotherhood. They found out that they stole a truck with bodies inside it. Meanwhile, Leo Fitz met with Holden Radcliffe and the latter showed him Aida, a Life-Model Decoy which would serve as a decoy target for Agents in battle. Fitz said they should wait since he did not know how the Director would use it. At the same time, Simmons found out that May helped Coulson and Mackenzie perusing Johnson. Simmons ordered her team to bring them back. Coulson and Mackenzie waited for Johnson as they were watching through the cameras how the Arayan Brotherhood made a deal with the Chinatown Crew over a mysterious box. Suddenly, they could not see the feed and then they saw the criminals killing each other. May's team came and used I.C.E.R.s to get the box. On Zephyr One, the Chinatown Crew members were threaded and May told Coulson the director wanted to speak with him.

The Tour
"I count on you to be one of my top advisors. There's no one better than you, truly." "Okay. So..." "But, when it comes to May and Daisy, you can't be objective. And to that, I take exception. So, you focus on being the best agent we got, and I'll focus on being the best Director I can."

- Jeffrey Mace and Phil Coulson

Director Jeffrey Mace called Phil Coulson and Melinda May to his office. He assured the two that he was not angry about Coulson chasing Daisy Johnson behind his back, but she was a problem, since S.H.I.E.L.D. was about to be re-exposure. Mace asked Coulson to accompanied him while he would do a tour to United States Congress members in the Playground in order they would fund S.H.I.E.L.D.. Meanwhile, with Jemma Simmons help, Alphonso Mackenzie and Leo Fitz were headed to a laboratory where the mysterious box contained Lucy Bauer was made. Upon arriving, the two were attacked by another man who threw Mackenzie into a reactor. Suddenly, Ghost Rider entered the room and killed the ghost, and Johnson came and freed Mackenzie. After Ghost Rider left, Mackenzie asked Johnson to come with him so they could take care of her, only to realize that Yo-Yo Rodriguez had been in contact with her all this time. They were angry at her for leaving them, but Johnson said she did what she needed to do and left. At the same time, May developed the same symptoms Chen from the Chinatown Crew had had. To retrain her, Coulson and her team tried to knock her out, but May resisted. But only when Mace came he used his Inhuman strength and durability to knock her out. By the end of the tour, Coulson asked Mace how he planned to help May, but Mace remained him that he was now the director, therefore he could not tell him. May was taken on a Quinjet away from the base.

Into the Lights
"And it won't work because there's an old friend back in town, here to deal with this threat and any other threat that comes our way. And last night, that old friend turned all the lights back on, saving countless lives. And that old friend is S.H.I.E.L.D."

- Jeffrey Mace

A group of Watchdogs, claiming to be Inhumans in order to incite fear and hate, caused a blackout in Miami, claiming that they would do the same thing to more major cities if the registration won't stop. Jeffrey Mace sent Phil Coulson, Leo Fitz and Alphonso Mackenzie to investigate the attack. As more and more cities went dark and the violence against Inhumans rised, Fitz figured out that an EMP was casuing the blackouts. The three went to a party and saved Yo-Yo Rodriguez from a Watchdogs team that went after her. They found out that the Watchdogs were behind the global attack and used the Inhumans list from the Sokovia Accords to track them down. Fitz found the location of the EMP device, so the four defeated the Watchdogs guards and brought back the lights to Miami. S.H.I.E.L.D. managed to stop the blackouts in the rest of the world Meanwhile, Jemma Simmons, with the help of Holden Radcliffe, saved Melinda May from her illness. After Coulson returned to the Playground, he suggested to Mace to publicly announce the re-legalization. Mace organized a press conference, where he revealed to the public that S.H.I.E.L.D. had stopped the blackouts and it will serve both Humans and Inhumans.

Working with Vigilantes
"So you may want to be solo, but forces beyond our control are driving us together. You don't need us? Fine. Right now, we need you."

- Phil Coulson to Daisy Johnson and Robbie Reyes

Phil Coulson failed to get more information about the incedent in Momentum Labs from Eli Morrow. Outside the prison, he and Alphonso Mackenzie noticed Robbie Reyes, whom Mackenzie knew as Ghost Rider. After a short car chase, the two managed to catch Reyes. On Zephyr One, however, Coulson freed Reyes from the Containment Module after learning they were both searching for the same things. Reyes agreed to work with them and managed to get from his uncle that before she had turned into a ghsot, Lucy Bauer was after a book called Darkhold. Suddenly, Mackenzie told to Coulson that JT James had broken tracking bracelet. Reyes came with the two to a warehouse, there they found Watchdogs soldiers. To thier supprise, they saw Jemma Simmons and Daisy Johnson. Ghost Rider brought to the four James alive. Later, Coulson offered to Johnson and Reyes an alliance with S.H.I.E.L.D. to find the Darkhold before Bauer would. At evening, Coulson and Simmons came to Holden Radcliffe's house to visit Melinda May and Leo Fitz, and also Radcliffe's assistant, Aida.

Coulson went to an operation to free Morrow from prison without Jeffrey Mace would know about it. He and May came to the prison, however, Bauer and other ghosts had come before them and caused the wardens to attack them. Mackenzie, Johnson and Reyes arrived to save them. Meanwhile, Mace, with the help of Simmons, had a debate with Senator Ellen Nadeer, during which he reveled to the world that he was an Inhuman. Reyes killed the rest of the ghosts, but Bauer freed all the Watchdogs prisoners, who were defeated by Coulson, May and Johnson. Bauer managed to kidnap Morrow.

Conflict with Ghost Rider
"It doesn't change the fact that we have no way to contain Mr. Reyes. He's also the only person we know who can take out Lucy Bauer. We need him." "He'll have to pay for what he did." "I agree. But today's not that day."

- Phil Coulson and Jeffrey Mace

Coulson and his team tried to find Eli Morrow in Momentum Labs, but Lucy Bauer had already left the place. Jeffrey Mace came to Zephyr One with a team to search for Daisy Johnson and Robbie Reyes, so Coulson hided them and Gabe Reyes inside a Containment Module under the plane. Mace, however, found them. Leo Fitz told Mace that he had found Morrow in an old Roxxon Oil Corporation facility. Suddenly, Reyes broke the Module's doors and transformed into Ghost Rider. He almost killed Mace, but his brother prevented it. After a short conversation with Coulson, Mace agreed that Reyes would come with S.H.I.E.L.D. to kill Bauer. There, Coulson asked May to take the Darkhold and hide it. Reyes killed Bauer, but an explosion inside the facility caused him, Coulson and Fitz to disappear. May and Mackenzie searched for them, but couldn't find them. Only after the two saw the bodies of four agents they realized Morrow had caused the explosion and received material production powers.

Interdimensional Experience
"She is the tech we need to save them."

- Melinda May to Holden Radcliffe

Jeffrey Mace did not allow Alphonso Mackenzie to investigate the Chinatown Crew about Eli Morrow's location. With nowhere else to turn and Mackenzie's and Daisy Johnson's sudden disappearance, May asked Holden Radcliffe's help to find a way to bring back Phil Coulson and Leo Fitz. She showed him the Darkhold but he refused to use it. Instead he suggested that his assistant, Aida, would use it, revealing that she was actually an Android. With the knowledge she read, Aida built a machine that opened an Interdenominational gate which showed Coulson and Fitz were in trouble. However, the two managed to return to Earth safely, Fitz, after learning that Mace had taken Jemma Simmons away, demanded to see her, only to be surprised to her and he reunited with her.

Battle at the Chinatown Crew Headquarters
"In case you haven't noticed, Phil, we're not a team that trusts. We're not a team at all." "Maybe you're right. But we damn well better become one if we're gonna stop Eli Morrow from blowing up half of Los Angeles."

- Jeffrey Mace and Phil Coulson

S.H.I.E.L.D. located Eli Morrow and his Chinatown Crew members in Los Angeles. After Phil Coulson revealed to Jeffrey Mace was an Android, he sent Daisy Johnson, Robbie Reyes and Yo-Yo Rodriguez to investigate Morrow's hideout. Reyes came into a hall where a large Quantum Battery full with energy from another dimension was placed. He managed to send the feed to Leo Fitz before he was trapped inside the box by his uncle. Fitz detected a material inside the box which could destroy half of Los Angeles if it would drop. Mace brought to the mission Holden Radcliffe and Aida to assist them deliver the box into another dimension with the Inter-Dimensional Gate. Fitz also realized that Morrow harnessed the energy from the other dimension and unknowingly cased earthquakes. As part of their plan, Coulson surrendered himself to Morrow as Fitz, Jemma Simmons, Radcliffe and Aida placed the Inter-Dimensional Gate beneath the box and Johnson tried to observe the earthquakes. Coulson tried to convince Morrow to stop his plan but since he did not listen, Coulson ordered the team to operate. He, Melinda May, Alphonso Mackenzie, Rodriguez and Mace defeated the Chinatown Crew members and threw Morrow into the box. Coulson tried to get Reyes out of the box, but as the Inter-Dimensional Gate gate opened, Reyes stayed to kill his uncle and he vanished with the box. Johnson tired to escape the scene, but as she landed near to crowd of journalists. Mace hurried to explain the Johnson had been a S.H.I.E.L.D agent all along. In the Playground, Coulson said to Johnson that he had wanted she would become the new Director. Johnson officially rejoined S.H.I.E.L.D. and Mace ordered Radcliffe to do his Life-Model Decoy experiments in their labs.

A Rogue LMD
"You know, I have to admit Jemma is much tougher than I had originally given her credit for." "Yeah, well, being in S.H.I.E.L.D. will do that to you."

- Jeffrey Mace and Daisy Johnson

At the Playground, Jeffrey Mace debriefed Phil Coulson, Leo Fitz, Alphonso Mackenzie, Holden Radcliffe and Melinda about the situation regarding the Darkhold. Coulson planned to have the book destroyed, while Fitz and Radcliffe would wipe out Aida's memory, since she could not be trusted. Mace then gave Daisy Johnson their next mission - to save the Inhuman held against his will by Senator Ellen Nadeer. Since Simmons had already figured out the Inhuman was the Senator's brother, Vijay, she, Mace and Johnson went to the Senator' home to find him, only to rescuing from the Watchdogs. However, Vijay left with his sister. Meanwhile, Aida resisting from being wiped from her memories and escaped. Finding also Nathanson's body, the team realized she was after the Darkhold. The LMD attacked the base by entering its system. After she found the book, Fitz and Radcliffe got back the control on the system and stopped Aida before she was about to leave. Mackenzie then cut off her head and the book was safe again.

Mace's Secret
"What do you want me to do?" "Same thing you've been doing. Defend S.H.I.E.L.D. to the public, play the hero. Keep the title, handle the politics. I never loved that part, anyway. But when it comes to operations, make no mistake. From now on, I'm calling the shots."

- Jeffrey Mace and Phil Coulson

During an appreciation ceremony for Daisy Johnson, a sniper tried to assassinate Jeffrey Mace. Phil Coulson, Alphonso Mackenzie, Mace and Burrows flew with a Quinjet to a safe house. However, the plane crashed in wood, killing Burrows. Glenn Talbot helped S.H.I.E.L.D. to find the three missing by also telling Leo Fitz and Jemma Simmons that Mace was not an Inhuman, but rather a person who used a special serum to gain abilities. The three faced a group of ex-HYDRA agents hired by the Watchdogs to kill Mace. Eventually, Johnson and Melinda May found and rescue them. At the Playground, Coulson clarified to Mace that from now on, he would make the orders while Mace would still be the face of S.H.I.E.L.D.

Infiltrate the Capitol Building
"Daisy now represents S.H.I.E.L.D. Everything has to be aboveboard." "But marching into the Capitol Building so Daisy can sign the Sokovia Accords? Senator Nadeer will be there. It seems risky." "We're all aware of the dangers, some of us more than others."

- Glenn Talbot, Jemma Simmons and Jeffrey Mace

Daisy Johnson decided to sign the Sokovia Accords in a hearing of the United States Congress. Phil Coulson saw an opportunity to implant surveillance cameras inside Ellen Nadeer's office. As Johnson, Jeffrey Mace and Glenn Talbot attended the hearing, during which Senator Nadeer blamed her and S.H.I.E.L.D. for breaking the law, Coulson and Yo-Yo Rodriguez were inside the office. However, the two were caught. Coulson realized that there was a leak inside of S.H.I.E.L.D., that led to Leo Fitz discovering that it was Holden Radcliffe. They arrested him, only to realize they had arrested his LMD.

Attack on the Watchdogs
"But it's not too late to do the right thing. Grab what you need. It's time to show the world what S.H.I.E.L.D. stands for."

- Jeffrey Mace

The Watchdogs kidnapped Billy Koenig. Knowing that the Watchdogs had taken him for the Darkhold, Couslon asked Daisy Johnson to identify the kidnappers. Johnson managed to identify the financier of the Watchdogs, Anton Ivanov. Coulson asked Sam Koenig where was the Darkhold, but he replied that only LT Koenig knew. After they recruited LT, she revealed that the book was hidden inside the Labyrinth. They arrived at the place, but as Sam recovered the Darkhold, Watchdogs arrived with Billy. Additionally, Leo Fitz and Jemma Simmons told Johnson that Melinda May had been replaced with an LMD. Johnson stopped LMD May from shooting Coulson. Then they rescued Billy, but Holden Radcliffe took the Darkhold and escaped. While Coulson and Alphonso Mackenzie were trying to find a way to locate May], Senator Ellen Nadeer was killed in an explosion in her office. Mace, Johnson, Fitz and Simmons investigated the scene and discovered that Tucker Shockley had visited the Senator prior to the explosion. Johnson caught him and interrogated him on Zephyr One. However, he revealed himself as an Inhuman and tried to use his powers to explode himself, but they managed to throw him out of the plane. Shockley was still alive, so the four came out with a plan to catch him. Johnson exploded Shockley with her powers, but as he was about the reform his body, he was trapped in gas state inside a container by Fitz and Simmons. Mace, on the other hand, was kidnapped by Anton Ivanov.

The team located Mace in a mining facility in Russia. Coulson confronted Ivanov, who saw Coulson responsible for the alien troubles on Earth. Johnson managed to hurt Ivanov severely. They found Mace, but Aida escaped with Radcliffe and May on a submarine. At the Playground, Fitz and Simmons discovered that Coulson, Johnson, Mackenzie and Mace had been replaced by LMDs during the mission.

Fight against the LMDs
"This is not a sacrifice play. You know why? Because I will beat them. You hear me? I know it. If for no other reason than this through all the insane crap we have gone through, the one thing I've known, without a doubt, the whole time is you and Fitz belong together."

- Daisy Johnson to Jemma Simmons

The LMDs planned to bring all the tacked Inhumans to the Playground in order to kill them. Meanwhile, Jemma Simmons discovered also Leo Fitz had been replaced by an LMD and deactivated it. While Simmons was hiding from the rest of the LMDs, Daisy Johnson also discovered the truth and convinced Simmons she was the real her. LMD Mace and LMD Coulson turned all the agents against Johnson and Simmons and they searched all over the base for the two. Johnson managed to destroy LMD Mace and LMD Mackenzie. Johnson and Simmons went with Davis, Piper and Prince to Zephyr One in order to escape the base. They convinced the LMD May to help them and she blew part of the base and destroyed LMD Coulson.

The Framework
"So you just plug yourself into these avatars?" "Hook up with our people and find out where on Earth their bodies are being held." "And rescue them." "That sounds easy. Will it be easy?" "They don't know."

- Piper, Daisy Johnson and Yo-Yo Rodriguez

On Zephyr One, the agents and Yo-Yo Rodriguez helped Daisy Johnson and Jemma Simmons entering the Framework, so they would find there the missing agents and free them from Aida. During that time, Jeffrey Mace's avatar died, killing the Director himself. The agents on the Zephyr were hunted by the Superior. Eventually, Johnson and Simmons managed to wake all the agents, with the exception with Alphonso Mackenzie, but Aida created for herself an Inhuman body.

From the Tin to the Bottom
As Phil Coulson, Melinda May and Leo Fitz were still shocked from their experience, Aida reveled herself to them and used her abilities to transport her and Fitz away from Ivanov Oil Platform. On Zephyr One, the agents located the missing agents' location and went to rescue them. They saved Coulson and May and brought them onboard, but surprisingly Aida saved the still plugged into the Framework Alphonso Mackenzie. They returned to the Playground and found it burned down. Glenn Talbot and his unit suspected the agents to be Life-Model Decoy and threatened them. Meanwhile, Aida lost her mind upon learning Fitz did not want to be with her. She used her Inhuman abilities to attack Davis and Prince, so the agents had to abounded the base and leave Aida behind. On their run, Yo-Yo Rodriguez entered the Framework to bring Mackenzie back.

Return of the Rider
"We were all in the Framework together. We understand how confusing and screwed-up that world is. And trust me, it's gonna take me years to process everything that happened in there. But the one thing that I don't need time to understand is that we are all in this together."

- Daisy Johnson to Leo Fitz

To their surprise, Robbie Reyes returned to Earth to get the Darkhold and kill Aida. Glenn Talbot informed Phil Coulson that there was a conference regarding S.H.I.E.L.D.'s future, with Aida's spawn Anton Ivanov attending. Together with Reyes, they found Talbot shot by Daisy Johnson' LMD. They retrieved the Darkhold from Aida's LMD army and planned their next move, after realizing Aida wanted to use Daisy Johnson to create a similar events which led to HYDRA's domination over the Framework world. In order to draw Aida to them, they returned to the Playground. They used Jemma Simmon's LMD and Leo Fitz so Aida would encounter Coulson, who with the powers generated by the Spirit of Vengeance managed to kill Aida. Yo-Yo Rodriguez managed to get Alphonso Mackenzie out of the Framework before it was deleted. Coulson handed Reyes the Darkhold and the latter returned to Hell dimension. However, following the years' events, Coulson and the others were fugitives once more and all the key agents were captured and put in a prison in space.

Facilities
Since the United S.H.I.E.L.D. (2015-present)
 * Theta Protocol Facility (Secret housing facility of Helicarrier No. 64)
 * The Cocoon (Training facility)
 * Retreat (Safe-House for powered people)
 * The Red Door
 * Thunderclap

Former Facilities
 * The Playground (Former primary HQ) (destroyed)
 * The Triskelion (Former primary HQ) (destroyed)
 * S.H.I.E.L.D. Headquarters (status unknown)
 * S.H.I.E.L.D. Airbase (status unknown)
 * The Hub (Operational planning and support) (presumed to be held currently by the United States Armed Forces)
 * The Slingshot (Study and disposal of dangerous technology) (status unknown)
 * The Fridge (High-security detainment and storage facility) (infiltrated by HYDRA)
 * The Sandbox (Study and disposal of hazardous or contagious material) (taken over by HYDRA)
 * S.H.I.E.L.D. Trauma Zentrum (Medical facility)
 * Providence (One of Nick Fury's secret S.H.I.E.L.D. facilities) (currently held by the United States Armed Forces)
 * The Cube (status unknown)
 * The Treehouse (taken over by HYDRA)
 * S.H.I.E.L.D. East African Headquarters (taken over by HYDRA)
 * S.H.I.E.L.D. Academy (sieged by HYDRA, status unknown)


 * S.H.I.E.L.D. Academy of Science and Technology (sieged by HYDRA, status unknown)
 * S.H.I.E.L.D. Training Facility (status unknown)
 * Maria Hill's Field Office (status unknown)
 * Barbershop Headquarters (taken over by HYDRA, destroyed)
 * The Rat (Prison facility) (status unknown)
 * Joint Dark Energy Mission Facility (destroyed)
 * S.H.I.E.L.D. Crater Investigation Site (temporary)
 * S.H.I.E.L.D. Base Camp (temporary)
 * The Guest House (formerly, destroyed)
 * The Coventry (formerly)
 * Shangri-La (formerly)
 * Labyrinth (compromised by the Watchdogs)
 * Camp Lehigh (formerly, destroyed)

There was a Wall of Valor located at every S.H.I.E.L.D. Academy.

Equipment and Technology
S.H.I.E.L.D. personnel have access to an extensive array of cutting edge technology at their disposal.

Weapons
Regular S.H.I.E.L.D. field agents are usually equipped with a 9mm pistol, usually a, or more recently, a. A military branch used for heavy security has access to military grade personal armaments. A few selected elite agents carry less conventional armaments, such as explosives, or bows. The S.H.I.E.L.D. project titled, "Phase 2", was dedicated to advancing alien technology weapons and reverse-engineer them into directed-energy weapons.

Pistols and Handguns

 * Smith & Wesson M&P: Standard sidearm of S.H.I.E.L.D. agents and Nick Fury.
 * Glock 17: Standard sidearm of S.H.I.E.L.D. agents prior to the Smith & Wesson M&P.
 * Smith & Wesson M&P Compact: Used by field agents in operations requiring higher mobility.
 * Glock 19: Primary sidearm of STRIKE Operatives and used by Hill.
 * SIG-Sauer P226: Carried by STRIKE Operatives and field agents; primary sidearm of Brock Rumlow.
 * M1911A1: Used by STRIKE commandos during the Battle of Washington, D.C. and carried by Robert Gonzales as his primary sidearm.
 * CAA Tactical RONI-SI1: Standard pistol carbine used by field agents.
 * Beretta 92FS: Used by Agents Hunter and Hartley while disguised as US Airmen.
 * Glock 26: Primary sidearm of Black Widow, who primarily used it while working with STRIKE and the Avengers.
 * FN FNX-9: Primary sidearm of Sharon Carter, who primarily used it during the HYDRA Uprising.
 * Heckler & Koch P30: Primary sidearm of Hawkeye, who primarily used it while working with the Avengers.
 * Walther PPK/S: Primary sidearm of the Koenig Brothers, who used it primarily to defend themselves from HYDRA agents.
 * Tokyo Marui Strike Warrior: Used by Melinda May to knock Andrew Garner into a Containment Module.
 * Smith & Wesson 910: Used by Skye to defend herself from Akela Amador.
 * Walther CP99: Stored in the armory of the S.H.I.E.L.D. Crater Investigation Site.

Submachine Guns

 * Heckler & Koch UMP45: Used by John Garrett and Grant Ward during the Raid of the Guest House.
 * Heckler & Koch MP5A3: Used by Lance Hunter during the Battle on the Maribel del Mar and obtained by Bobbi Morse and Joey Gutierrez during the Attack on the HYDRA Castle.
 * FN P90: Stored in the armory of the S.H.I.E.L.D. Crater Investigation Site.

Shotguns

 * : Used by various S.H.I.E.L.D. agents, most notably by engineers and technicians.
 * : Used by Lance Hunter and Phil Coulson during the kidnapping of Thomas Ward.

Assault Rifles and Carbines

 * : Primary assault rifle of S.H.I.E.L.D. operatives during combat and strike operations; primarily used before the S.H.I.E.L.D. Civil War before being phased out in favor of the Tavor TAR-21. This carbine was later re-introduced into S.H.I.E.L.D.'s arsenal following the Inhuman War.
 * : Primary assault rifle of S.H.I.E.L.D. operatives working under Robert Gonzales' faction and later all S.H.I.E.L.D. operatives following the S.H.I.E.L.D. Civil War under Director Coulson.
 * : Standard firearm for STRIKE operatives, especially those raiding the Lemurian Star.
 * Colt LE Carbine: Used by S.H.I.E.L.D. operatives to secure the area during HYDRA's Kidnapping of Charles Hinton.
 * : Used by S.H.I.E.L.D. security guards working under Robert Gonzales on the Illiad.
 * Steyr AUG A3: Used by STRIKE commando Brock Rumlow.
 * Daniel Defense DDM4 MK18: Prepared by Lance Hunter to use during the Attack on the Retreat.
 * M16A4: Stored in the armory of the S.H.I.E.L.D. Crater Investigation Site.
 * SIG-Sauer SG552: Stored in the armory of the S.H.I.E.L.D. Crater Investigation Site.

Sniper Rifles

 * Nemesis Arms Vanquish: Used by Grant Ward to aim at Mike Peterson in the case that he needed to be eliminated; also used by Skye to terminate Donnie Gill during the Battle on the Maribel del Mar.
 * : Used by Agents Triplett and Hunter to attempt to assassinate Carl Creel.
 * Desert Tactical Arms Stealth Recon Scout: Used by Grant Ward to provide overwatch during the hostage exchange between S.H.I.E.L.D. and Centipede on the bridge.
 * Remington 700PSS: Stored in the armory of the S.H.I.E.L.D. Crater Investigation Site.

Machine Guns

 * : Mounted under the cockpit of all Quinjets.
 * General Dynamics GAU-22/A: Mounted on the hull of F-35 Lightning II fighter jets.
 * General Dynamics M197 Vulcan: Mounted under the cockpit of military S.H.I.E.L.D. Helicopters.
 * Phalanx CIWS: Mounted on the Project Insight Helicarriers.
 * Browning M2HB: Mounted on an automated turret defending Providence.

Launchers

 * Olin Flare Gun: Used by Leo Fitz to fire a flare into the Monolith as a signal for Jemma Simmons.
 * Orion Flare Gun: Used by Leo Fitz to fire a flare at Hive, who was possessing Will Daniels' body, in order to incinerate and kill him.
 * RM Equipment M203PI: Mounted on M4A1 carbines; used by Phil Coulson and Antoine Triplett to defend Providence from US Special Forces.
 * Fabrique Nationale EGLM: Mounted on FN SCAR-H rifles; used by John Garrett to defend himself against an attack from Deathlok.
 * Milkor MGL Mk 1L: Used by Lance Hunter with an Electric Net Grenade to apprehend Vin-Tak.
 * M136 AT4: Used by a STRIKE commando on-board a Project Insight Helicarrier.
 * Airtronic RPG-7: Used by Nick Fury to prevent the takeoff of a fighter jet armed with a nuclear missile.
 * MM1 Grenade Launcher: Used by operatives attempting to take Bruce Banner into custody in India.

Explosives

 * M67 Fragmentation Grenade: Carried by STRIKE operatives.
 * 40mm Grenade: Ammunition for the M203, EGLM, MGL, and MM1.
 * M18 Smoke Grenade: Used to provide cover, such as during the raid on the government warehouse.

Blades and Melee Weapons

 * Taser Rod: Used by STRIKE commandos to subdue and stun targets
 * Protecop BOSH007 Anti-Riot Shield: Used by STRIKE commandos for personal protection against thrown debris and small-caliber bullets.

Special Weapons

 * Destroyer Armor Prototype Gun
 * Night-Night Gun and Pistol
 * Thunderstick
 * I.C.E.R.s
 * Taser Projectile Launcher
 * Overkill Device
 * Taser Rod
 * Taser Disk
 * Taser Pin
 * Electric Net Grenade
 * Wristbow
 * Cloaked Gun
 * Shotgun-Axe

Vehicles
S.H.I.E.L.D. maintains fleets of Acura and Lexus vehicles for the regular deployment of field agents and scientists. S.H.I.E.L.D. editions of the Acura MDX, Acura TL, Acura ZDX; and Lexus GS 350, Lexus GX 460, and Lexus IS, are painted in black, emblazoned with the S.H.I.E.L.D. seal, and are equipped with sophisticated surveillance technology. The military arm of S.H.I.E.L.D. uses a range of surface vehicles suitable for urban security, and aircraft with combat capabilities extending to fighter jets and helicopters. This branch also has access to exclusive aircraft types. Former
 * Helicarrier No. 64 - Airborne aircraft carrier and command unit
 * Iliad - Aircraft carrier and command unit; headquarters of Robert Gonzales' faction until reunification
 * Modified 1962 Chevrolet Corvette (aka "Lola") - VTOL car
 * S.H.I.E.L.D. Quinjets - Armed aircraft
 * S.H.I.E.L.D. Motorcycles
 * S.H.I.E.L.D. SUVs
 * Transporters
 * Zephyr One
 * CXD 23 Airborne Mobile Command Station (S.H.I.E.L.D. 6-1-6, aka "The Bus") - Airborne command unit
 * Insight Helicarriers (IN-01, IN-02, IN-03) - Next-generation armed Helicarriers
 * Lemurian Star - Mobile satellite launch platform
 * Nick Fury's SUV
 * S.H.I.E.L.D. Railbikes
 * S.H.I.E.L.D. UAVs
 * S.H.I.E.L.D. Jump Jets
 * S.H.I.E.L.D. Helicopters

Misc.
S.H.I.E.L.D. scientists work tirelessly both in the lab and in the field to develop new equipment, technologies and compounds on the fly.

S.H.I.E.L.D. ID Cards
S.H.I.E.L.D. issues personal ID Cards for each of their agents, displaying their name, title, date of birth, ID number, date of issue, date of expiration, and in some cases their Clearance Level.

After the Fall of S.H.I.E.L.D., ID Cards were replaced by special lanyards. Those lanyards were replaced by new Clearance Level color based cards.

S.H.I.E.L.D. Files
S.H.I.E.L.D. maintains files on their agents, people of interest, objects, events, places and various other things.

During the Battle of the Triskelion, Natasha Romanoff, with the assistance of Nick Fury and Alexander Pierce, dumped all of S.H.I.E.L.D.'s and HYDRA's files onto the Internet. Multiple non-electronic S.H.I.E.L.D. files survived the Fall of S.H.I.E.L.D. and either fell into the hands of non-S.H.I.E.L.D. entities or S.H.I.E.L.D. itself.

S.H.I.E.L.D. Codes
The following is a list of codes used by S.H.I.E.L.D..
 * 0-8-4, an object of unknown origin.
 * Clearance Level, the level of a S.H.I.E.L.D. agent.
 * The Index, a short-list of people with special powers.
 * Priority Red, heavy security

Protocols
 * Protocol ASTA06, destruction of the Iliad and its cargo
 * Full Eclipse Protocol
 * Odyssey Protocol, emergency evacuation of a team.
 * Silhouette Protocol
 * Theta Protocol, re-activation of Helicarrier No. 64
 * Contingency Plan Foxhole, evacuating the Director to a safe house

S.H.I.E.L.D. Projects
The following is a partial list of projects run by S.H.I.E.L.D..
 * Life-Model Decoy Program (abandoned)
 * Avengers Initiative (2008-2012)
 * Phase 2 (2012)
 * Project P.E.G.A.S.U.S. (2010-2012)
 * Project Mr. Blue (2010)
 * Project T.A.H.I.T.I. (2009-2014)
 * Project Insight (2012-2014)
 * Caterpillars (2015-2016)

S.H.I.E.L.D. Missions
"S.H.I.E.L.D.'s whole infrastructure is based on the hierarchy and compartmentalization of intelligence. Every agent can't have the intel on every mission. Makes the entire organization vulnerable."

- Phil Coulson


 * For the list: List of S.H.I.E.L.D. Missions

First Insignia
The first version of the S.H.I.E.L.D. insignia (and its variants) was primarily used from its formation in 1949 until mid-2012 when the second insignia was first introduced. It retained limited use until S.H.I.E.L.D.'s collapse in 2014.

Second Insignia
This version of the S.H.I.E.L.D. insignia (and its variants) has been in use since its introduction in mid-2012. It was used after S.H.I.E.L.D.'s collapse by Phil Coulson's S.H.I.E.L.D. faction and retained primary use after his faction unified with a faction led by Robert Gonzales in 2015.

Gonzales' Faction's Insignia
This alternate version of the S.H.I.E.L.D. insignia was used by the reorganized faction led by Robert Gonzales after S.H.I.E.L.D.'s collapse in 2014.

Allies

 * Avengers
 * Thor
 * Tony Stark/Iron Man
 * Bruce Banner/Hulk
 * Sif
 * Jane Foster
 * Darcy Lewis
 * Thaddeus Ross
 * Pepper Potts
 * James Rhodes/War Machine
 * Sam Wilson/Falcon
 * Elliot Randolph
 * Matthew Ellis
 * Advanced Threat Containment Unit
 * Rosalind Price †
 * Glenn Talbot
 * Luther Banks †
 * Robbie Reyes/Ghost Rider

Enemies

 * Obadiah Stane/Iron Monger †
 * Samuel Sterns (imprisoned)
 * Ivan Vanko/Whiplash †
 * Justin Hammer (imprisoned)
 * Hammer Drones (destroyed)
 * Emil Blonsky/Abomination (imprisoned)
 * Georgi Luchkov
 * Destroyer (confiscated)
 * Sofia †
 * Loki
 * Chitauri
 * Vanchat (imprisoned)
 * Rising Tide
 * HYDRA
 * Wolfgang von Strucker †
 * List †
 * Alexander Pierce †
 * Daniel Whitehall †
 * Gideon Malick †
 * Grant Ward †
 * Sunil Bakshi †
 * Octavian Bloom †
 * Winter Soldier
 * Brock Rumlow †
 * Jack Rollins
 * Jasper Sitwell †
 * Marcus Scarlotti (imprisoned)
 * Kebo †
 * Werner von Strucker (in coma)
 * Giyera †
 * Lucio †
 * Senator Stern (imprisoned)
 * Centipede Project
 * John Garrett †
 * Ian Quinn
 * Debbie †
 * Scorch †
 * Edison Po †
 * Kaminsky
 * Raina †
 * Camilla Reyes (imprisoned)
 * Franklin Hall (believed deceased)
 * Norse Paganists
 * Jakob Nystrom (imprisoned)
 * Petra Larsen (imprisoned)
 * Lorelei
 * Marcus Daniels †
 * Donnie Gill (believed deceased)
 * Calvin Zabo
 * Agent 33 †
 * Vin-Tak
 * Slicing Talons
 * Karla Faye Gideon
 * David Angar
 * Francis Noche
 * Wendell Levi
 * Ultron †
 * Ultron Sentries †
 * Afterlife Inhumans
 * Jiaying †
 * Gordon †
 * Androvich †
 * Watchdogs
 * Anton Ivanov
 * Felix Blake
 * Ellen Nadeer †
 * Briggs (imprisoned)
 * Yuri Zaikin (imprisoned)
 * Viktor Orlov
 * Tucker Shockley (imprisoned)
 * Chinatown Crew
 * Chen †
 * Hive †
 * Alisha Whitley †
 * Primitives
 * JT James/Hellfire
 * Lucy Bauer †
 * Eli Morrow †
 * Holden Radcliffe †
 * Aida †
 * Life-Model Decoys
 * Melinda May (Life-Model Decoy) †
 * Holden Radcliffe (Life-Model Decoy) †
 * Phil Coulson (Life-Model Decoy) †
 * Alphonso Mackenzie (Life-Model Decoy) †
 * Jeffrey Mace (Life-Model Decoy) †
 * Leo Fitz (Life-Model Decoy) †
 * Daisy Johnson (Life-Model Decoy) †

Trivia

 * S.H.I.E.L.D. is arguably the most recurring staple in the Marvel Cinematic Universe, as it has been mentioned or featured in some form or another in almost every MCU product.

Behind the Scenes

 * A S.H.I.E.L.D. film was planned but it was eventually scrapped and turned into Agents of S.H.I.E.L.D..