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

TALK PAGE

"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., was originally a United States extra-governmental military counter-terrorism and intelligence agency. Founded in the wake of 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 all kinds of superhumans, demigods, and extraterrestrials. But all the problems S.H.I.E.L.D. had to solve eventually led to the formation of the Avengers, a group of superheroes that saved 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 destroyed, 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.

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 agency 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, Dr. Henry 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.

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 couldn't 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 the E.N.L.. 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.

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

In 2009, 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 flied 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 Ross and his unit 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 his troops; Banner then transformed into the 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, whose unit was preparing to depart in search for the 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 end 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 didn't 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

Sixty-five 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 he awoke he quickly realized it wasn't real and escaped into the streets of a 2011 New York City. In Times Square, Rogers encounters Nick Fury who told him that he's been "asleep" for nearly seventy years. Steve then realized that many of his old friends were very likely dead, including his love interest, Peggy Carter.

Attack on 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".

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., F.B.I., and C.I.A. 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 believes he has set up the small, highly trained team of agents to tackle the cases that haven’t been classified yet. The team originally consists of Coulson, May, Grant Ward, Leo Fitz and Jemma Simmons. They later recruited Skye to the team 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 Kwan 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 Kwan. 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 over-dose.

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. The Jotunheim Beast apparently continued to run freely through London.

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 was attacked by HYDRA assassin Winter Soldier and later captured by the STRIKE team. Thanks to Maria Hill, Roger, 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, Coulon'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 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, 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, Coulon 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 actually 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.

Redeemed
"Sometimes we want things simpler than they actually are, but the tough reality is, we are complex creatures. And I've come to understand something that world must, as well. There is a difference between S.H.I.E.L.D. and HYDRA. One was an organization built on protection, and the other world domination."

- Christian Ward

Though no longer targeted by Talbot's division, S.H.I.E.L.D. still had to operate from the shadows in its fight against HYDRA.

Coulson had Agent May and a team track down Grant Ward following his escape at Senator Ward's request. Though they did not capture Ward in Boston, Sunil Bakshi was captured and put into their custody.

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 City Blueprints. However, while there, the team was ambushed by HYDRA and Triplett was fatally 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 didn't 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.

The Inhuman Threat
"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 hip, and Lance Hunter set off the alarm. Coulson and Gonzales see Raina and Gordon through the security cameras, and Gonzales realizes that they are looking for their special cargo. Just as the teleporter and Raina discovered the location of the cargo, May and Morse found them, forcing them to teleport back to their base. Later, at the Playground, Gonzales' people successfully found the Inhuman's base. 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.

Facilities
Since the United S.H.I.E.L.D. (2015-present)
 * The Playground (Current primary HQ)
 * Theta Protocol Facility (Secret housing facility of Helicarrier No. 64)

Former Facilities
 * The Triskelion (Former primary HQ) (destroyed)
 * S.H.I.E.L.D. Headquarters
 * S.H.I.E.L.D. Airbase
 * The Hub (Operational planning and support) (presumed to be held by the United States Armed Forces)
 * The Slingshot (Study and disposal of dangerous technology)
 * 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) (held by the United States Armed Forces)
 * The Cube
 * 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
 * S.H.I.E.L.D. Academy of Science and Technology (sieged by HYDRA)
 * S.H.I.E.L.D. Training Facility
 * Maria Hill's Field Office
 * Barbershop Headquarters (taken over by HYDRA, destroyed)
 * 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)
 * The Coventry (formerly)
 * Shangri-La (formerly)

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

Paraphernalia
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 laser weapons.

Regular Weapons

 * Pistols and Handguns
 * Smith & Wesson M&P
 * Smith & Wesson M&P Compact
 * Smith & Wesson 910
 * Glock 17
 * Glock 26
 * SIG-Sauer P226
 * Walther PPK/S
 * CAA Tactical RONI-SI1
 * FN FNX-9


 * Submachine Guns
 * Heckler & Koch UMP45
 * Heckler & Koch MP5A3


 * Shotguns
 * Remington 870


 * Rifles & Carbines
 * Colt M4A1
 * IWI Tavor TAR-21
 * FN SCAR-H


 * Assault Rifles
 * M4A1
 * Heckler & Koch HK416


 * Sniper Rifles
 * Nemesis Arms Vanquish
 * Desert Tactical Arms Stealth Recon Scout
 * Remington Mk. 13 Mod 5


 * Machine Guns
 * Browning M2HB
 * General Dynamics GAU-22/A

Special Weapons

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

Vehicles
S.H.I.E.L.D. maintains a fleet of Acura vehicles for the regular deployment of field agents and scientists. S.H.I.E.L.D. editions of the Acura MDX, Acura TL, and the Acura ZDX are painted in black and 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
 * 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
 * CXD 23 Airborne Mobile Command Station (S.H.I.E.L.D. 616, 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.

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.

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.
 * Odyssey Protocol, emergency evacuation of a team.
 * Full Eclipse Protocol
 * Silhouette Protocol
 * Theta Protocol
 * Protocol ASTA06

S.H.I.E.L.D. Projects
The following is a partial list of projects run by S.H.I.E.L.D..
 * Avengers Initiative (2008-2012)
 * Phase 2 (2012)
 * Project P.E.G.A.S.U.S. (2011-2012)
 * Project Mr. Blue (2011)
 * Project T.A.H.I.T.I. (2009-2014)
 * Project Insight (2012-2014)
 * Caterpillars (2015-)

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

Strategic Scientific Reserve
This insignia was used by the Strategic Science Reserve from its creation in 1940. It retained its use after the SSR was absorbed into S.H.I.E.L.D. as one of its scientific research and development subdivisions until it was dissolved and fully absorbed into other S.H.I.E.L.D. subdivisions several years later.

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 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/Iron Patriot
 * Sam Wilson/Falcon


 * The Great Alliance Force

Enemies

 * Obadiah Stane/Iron Monger †
 * Samuel Sterns (imprisoned and being studied for Project Mr. Blue)
 * 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
 * Alexander Pierce †
 * Brock Rumlow
 * Jack Rollins
 * Jasper Sitwell †
 * Centipede Project
 * John Garrett †
 * Ian Quinn
 * Debbie †
 * Scorch †
 * Edison Po †
 * Grant Ward
 * Raina
 * Camilla Reyes (imprisoned)
 * Franklin Hall (believed deceased)
 * Norse Paganists
 * Jakob Nystrom (imprisoned)
 * Petra Larsen (imprisoned)
 * Lorelei
 * Marcus Daniels †

Video Games Only

 * A.I.M.
 * Kearson DeWitt
 * Crimson Dynamo
 * R.A.I.D.
 * Serpent Society
 * U.L.T.I.M.A.T.U.M.

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.
 * 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..