After World War II, the Strategic Scientific Reserve evolved into S.H.I.E.L.D., but was soon infiltrated by HYDRA operatives, starting with Arnim Zola in Operation Paperclip. For the next several decades, HYDRA grew within S.H.I.E.L.D.'s ranks, manipulating the agency and using its unlimited resources to suit their plans.
In 2014, the infiltration was exposed during Project Insight, and HYDRA, in an effort to save itself, started purging all S.H.I.E.L.D. facilities of non-HYDRA aligned individuals. After HYDRA's existence was revealed, the War on HYDRA began, as the Avengers and the reformed S.H.I.E.L.D. fought to dismantle HYDRA. In 2016, the United States Armed Forces seemingly destroyed HYDRA, although several high-ranking members survived the attack and went underground.
Originally founded by Johann Schmidt as an advanced weapons division of the Nazi Schutzstaffel, HYDRA became an independent terror group bent on global domination during World War II. The majority of Schmidt's plans revolved around the Tesseract, an Infinity Stone that had been left on Earth by Odin centuries ago.
The group came into constant conflict with Captain America, who successfully disabled several of their facilities before confronting Schmidt at his headquarters. In the battle, Schmidt disappeared after physically handling the Tesseract, HYDRA was left without a leader and fell on the verge of collapse.
Shortly after the end of the war, the peacekeeping agency S.H.I.E.L.D. was founded. Through Operation Paperclip, former HYDRA scientist Arnim Zola was recruited into S.H.I.E.L.D., but his recruitment proved to have dire consequences in the future. As a member of S.H.I.E.L.D., Zola sought out and provided access into the agency for several HYDRA operatives and loyalists that managed to escape justice after WWII. From within S.H.I.E.L.D., the new HYDRA grew like a parasite and slowly regained power.
Shortly after the war, Arnim Zola was able to find his former test subject Bucky Barnes who survived the fall from Zola's train in 1945, though he lost his left arm. Using S.H.I.E.L.D.'s resources, Zola continued his experiments on Barnes, brainwashing him and giving him the new cybernetic arm to replace his lost limb. Now blindly loyal to Zola and enhanced with another version of the Super Soldier Serum, Barnes became HYDRA's new fist, eventually gaining the nickname Winter Soldier.
In 1955, Daniel Sousa came to suspect that S.H.I.E.L.D. had been infiltrated, so he submitted a report to the CIA, who did not respond. Wilfred Malick, a HYDRA plant in S.H.I.E.L.D. who had become Sousa's superior, found out about the report and sent an agent to kill him while he was delivering a piece of technology to Howard Stark. The official report said that Russia had sent agents to kill Sousa, and he became known as the first fallen agent of S.H.I.E.L.D., a hero to agents such as Phil Coulson.
Over the next decades, HYDRA managed to rebuild much of its former strength. Secretly feeding crises around the globe, HYDRA created a world full of terrorist threats, wars, and dictators. And when some S.H.I.E.L.D. operatives would try to stop the terrorists, HYDRA would eliminate them, like one of S.H.I.E.L.D.'s founders, Stark, and his wife Maria in 1991, though the world believed that they died in a car accident.
In 1972, Dr. Zola was diagnosed with a terminal illness. However, since he was one of the greatest scientific geniuses in the world, the leaders of S.H.I.E.L.D. decided to save his mind. Shortly before his physical death, Zola's consciousness was downloaded into a computer system located deeply beneath Camp Lehigh, S.H.I.E.L.D.'s first base. Continuing his existence as an artificially intelligent user interface, Zola created the 'Zola-algorithm' which was used by HYDRA to identify and target potential threats to its interests. Eventually, almost half of S.H.I.E.L.D. was composed of HYDRA's undercover agents or those who were corrupted and swore allegiance to HYDRA.
Alexander Pierce, the leader of HYDRA operatives in S.H.I.E.L.D., eventually became one of the agency's directors, and a member of the World Security Council. During his tenure, Project Rebirth was restarted as the Bio-Tech Force Enhancement Project which included new directions such as Gamma Radiation, the WSC pushed ahead with Phase 2, a project continuing development of Tesseract-powered weapons, and pushed for Emil Blonsky to be included in the Avengers Initiative. Senator Stern served as HYDRA's mole inside the United States Senate and attempted to pressure Tony Stark into surrendering the Iron Man technology. Agent Jasper Sitwell was in charge of ensuring that various S.H.I.E.L.D. teams contained a minimum number of HYDRA agents, and acquired and studied various technologies including Mjølnir during Thor's time as a mortal and Chitauri technology after the Battle of New York. Among the researched tech was the Loki's Scepter and at least one Leviathan corpse which were secretly moved by Baron Strucker and Doctor List to a HYDRA Research Base in Sokovia. Agent John Garrett fed biotechnology secrets to the Centipede Project, including gamma-altered Super Soldier Serum and Extremis, as well as Chitauri injection systems.
Troubles in Washington
After the Battle of New York, the World Security Council granted S.H.I.E.L.D. more funds to invest in homeland security, for which "Project Insight" was created, a security network formed by three heavily-armed Helicarriers to protect the nation. However, the leaders of HYDRA planned to use the Helicarriers to eliminate anyone who had been distinguished as a threat by Arnim Zola's algorithm.
As Nick Fury discovered that something dubious was going on, he secretly hired the French mercenary Georges Batroc and his gang of pirates to hijack the Lemurian Star, a S.H.I.E.L.D. ship related to Project Insight. During the rescue mission, the Black Widow would then have a chance to secretly recover confidential files.
After recovering the data, Fury attempted to open the files but discovered they were highly protected. He persuaded Pierce, his friend, to delay Project Insight as S.H.I.E.L.D. could have been compromised, not knowing that Pierce was in fact HYDRA's top undercover agent in S.H.I.E.L.D.
A few hours after Fury's conversation with Pierce, a group of HYDRA agents disguised as cops attempted to kill Fury, but when he escaped them, the Winter Soldier intervened. Fury again managed to escape, though he was heavily wounded, and went to the apartment of the recently revived Steve Rogers, Captain America. When Rogers came home, Fury told him that S.H.I.E.L.D. had been compromised, when the Winter Soldier, who had followed Fury to the apartment, shot him from behind. Before falling unconscious, Fury gave Rogers the flash drive containing the files Black Widow had recovered.
Later, at the hospital, Fury apparently dies as his heart stops. However, that was only a ruse orchestrated by Fury himself. Agent Maria Hill asked to take care of the body and took him to a secret location for Doctor Fine to take care of his wounds. When Agent Brock Rumlow of the STRIKE team, actually an undercover HYDRA operative and Pierce's right hand man, came to the hospital to take Rogers to Pierce, Rogers hid Fury's USB in a vendor machine.
When Rogers arrived at the Triskelion, Pierce questioned him about the circumstances of Fury's death. Though Pierce told him that he and Fury were old friends, Rogers decided not to trust him and left his office. Pierce then gave the order to Rumlow and his men to capture Rogers.
The Manhunt Begins
As Rogers came into the elevator, Rumlow and a dozen other STRIKE team members joined him there. However, Rogers noticed that something was wrong, and they attacked him. When he defeated them, another team of heavily armed S.H.I.E.L.D. agents attempted to stop him, but he escaped by jumping out of the elevator to avoid arrest. After surviving the fall he drove away on a motorcycle, though agent Jasper Sitwell, another HYDRA mole, set up a roadblock and sent a Quinjet to stop him. When Rogers escaped, Pierce told the S.H.I.E.L.D. agents at the Triskelion that Rogers is refusing to share information about Fury's death, and that he has become a fugitive. Later that night, the Winter Soldier came to Pierce's apartment, and he gave him orders to kill Rogers.
Hunt for the Clairvoyant
Meanwhile, Phil Coulson and his team were actively hunting the mysterious Clairvoyant, the man behind the Centipede Project, a scientific research and development group bent on recreating the super soldier. As Mike Peterson was transformed into the Deathlok and attacked some of S.H.I.E.L.D. agents, they tracked him to Pensacola, Florida, where he managed to escape, but they discovered Thomas Nash, a vegetative man on life support who introduced himself as Clairvoyant. He was immediately shot by Grant Ward, a HYDRA mole, who did that on the order of the real Clairvoyant, John Garrett.
The Truth Revealed
Back at the hospital, Steve Rogers was approached by Natasha Romanoff, who retrieved Nick Fury's USB some time earlier. Romanoff told Rogers about the Winter Soldier, a mysterious assassin who was responsible for the attack on Fury. When they went to an Apple store and tried to use one of the computers to see if there was any valuable information on the flash drive, Romanoff was unable to open the files. However, she managed to find the location where the USB could be unlocked, somewhere in New Jersey.
After evading the STRIKE team that was chasing them, Rogers and Romanoff arrived at Camp Lehigh, where Rogers was trained during World War II. Beneath the camp they discovered the old S.H.I.E.L.D. outpost housing dozens of old computers, but fitted with a modern USB interface. The computers came to life, revealing the digitized consciousness of Arnim Zola, who revealed them HYDRA's plan for world domination. While Zola was talking, HYDRA's operatives in S.H.I.E.L.D. launched two missiles at the base, blowing it up. However, Rogers and Romanoff managed to survive the explosion and found refuge at the apartment of Sam Wilson.
With Wilson's help, Rogers and Romanoff tracked down and interrogated Jasper Sitwell who revealed that the Project Insight was designed to eliminate millions of potential threats to HYDRA on the massive scale. Before they couls use Sitwell to get them inside the Triskelion to stop HYDRA, they were attacked by the Winter Soldier, who assassinated Sitwell. In the subsequent battle against HYDRA enforcers, Rogers managed to unmask the Winter Soldier and found out that Bucky Barnes was the one under the mask. Rogers, Romanoff and Wilson then were apprehended by the STRIKE team led by Brock Rumlow, but before STRIKE operatives could get rid of them, they were rescued by Maria Hill.
- "S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA. Alexander Pierce is their leader. STRIKE and Insight crews are HYDRA as well. We don't know how many more, but I know they're in the building, they could be standing right next to you. They almost have what they want: absolute control."
- ―Captain America[src]
Recruiting Captain America, Black Widow, Falcon, and Maria Hill to his cause, Nick Fury created a way to destroy the Insight Helicarriers. While Hill, Captain America, and Falcon dealt with the Helicarriers, he and Black Widow dealt with Alexander Pierce. As the Helicarriers fell, one of them veered into the Triskelion, severely damaging the building. During the battle, many members of the World Security Council were killed and a message was sent out, revealing the truth about the HYDRA infiltration.
Later, on the Bus, Leo Fitz discovered a secure line used by Melinda May. Believing her to be a traitor, Phil Coulson and Skye accused her of treachery, not knowing that she was actually talking with Director Nick Fury. Suddenly, the S.H.I.E.L.D. technicians at the Hub, on the orders of Victoria Hand, hijacked the control of the Bus and rerouted it for the Hub. Hand believed that Coulson and his team were HYDRA and ordered her agents to eliminate them all when the plane touched the ground. She also sent a pair of S.H.I.E.L.D. drones to attack and destroy John Garrett's plane. The same day, after the hijacking of the Bus' controls, the plane was flying toward the Hub. After surviving the attack from two S.H.I.E.L.D. drones, John Garrett boarded the Bus. Garrett and Coulson's team infiltrated the Hub with the intention of destroying it, thinking Hand to be HYDRA; it was eventually revealed, however, that the Battle of the Hub was largely staged, as Hand and a handful of agents had realized something was afoot and were secretly working against HYDRA.
- "Captain America has defeated the Helicarriers at the Triskelion. But his status is unknown."
"And S.H.I.E.L.D. has fallen."
"HYDRA factions have taken control of our east African headquarters and the Treehouse. And those are just the ones we know of."
"It's gonna be a scramble, a power grab."
- ―Victoria Hand and Phil Coulson[src]
Exposed, HYDRA immediately began covering their tracks, beginning on purging entire S.H.I.E.L.D. facilities of non-HYDRA agents and loyalists. While they successfully took over the Treehouse and the S.H.I.E.L.D. East African Headquarters, their attempted takeover of the Hub was thwarted by Phil Coulson and his team, aided by the revelation of Victoria Hand's true loyalties. Coulson's efforts led to the capture of HYDRA operative John Garrett, who managed to escape when Grant Ward murdered Agent Hand. S.H.I.E.L.D. loyalists managed to defeat HYDRA's operatives at the Cube, forcing them to retreat. A fierce battle was fought for the control of the aircraft carrier Iliad, but HYDRA's moles were ultimately defeated. HYDRA brainwashed Donnie Gill and used him as a one-man army in order to take the Sandbox.
The S.H.I.E.L.D. Academy was under assault by HYDRA forces, with the terrorists using an enhanced individual to assist them, when Tomas Calderon acquired a fleet of Quinjets to evacuate Anne Weaver and many loyal to S.H.I.E.L.D. to the safety of the Iliad.
In light of the new information, the U.S. government questioned the organization's existence in several hearings. As a direct result of the events, Captain America and the Black Widow both left S.H.I.E.L.D., along with many other agents. Eventually, because of how deep HYDRA's infiltration in S.H.I.E.L.D. was, the agency was internationally labeled a terrorist organization.
Following Ward's assassination of Agent Hand, Ward then freed Raina from a prison and took her to meet Garrett, who revealed to her that he was the Clairvoyant, at HYDRA's base in Havana, Cuba to continue the Centipede Project. The Cube was returned to S.H.I.E.L.D.'s custody, but the Fridge was captured and raided by Garrett, Ward, and their men. Many advanced weapons, including the Peruvian 0-8-4 and the Berserker Staff, fell into the hands of HYDRA.
When Victoria Hand redirected the Bus towards the Hub, no one knew the identity of the Clairvoyant, so Grant Ward convinced Phil Coulson to have Skye put all of the team's secret information and mission assessments on a hard drive. Ward was given this hard drive to protect; no one knew that he was a HYDRA agent.
Later, at the Barbershop Headquarters, Raina learned that only Skye could decrypt the hard drive and told John Garrett. The hard drive contained information about GH.325, the miracle drug that revived Coulson and Skye, which the Centipede Project wanted for their soldiers. Garrett commissioned Ward to get Skye or the decryption code.
Ward went to Providence thinking that he convinced Skye that the others needed her to decrypt the hard drive; he did not know that she knew he was a double-agent after she discovered the body of Eric Koenig. Skye went with Ward because she cared about him and wanted to know how he could betray them.
Skye lied, telling Ward that the hard drive was location-based, taking him to Ruthie's Skillet, where she tried to escape. Deathlok, Ward's back-up, caught her and, after inducing a heart attack in Ward, got Skye to decrypt the drive. Finally, Phil Coulson, with Maria Hill as a distraction, saved Skye by dropping out the Bus in Lola.
- "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."
- ―Phil Coulson and Melinda May[src]
The Centipede Project recruited Ian Quinn who proposed to the United States Armed Forces the making of Deathlok Soldiers to aid in the War on Terror, especially after S.H.I.E.L.D. was branded a terrorist organization by the international community. Quinn did not tell the government that the handlers of the soldiers had their family members kidnapped by HYDRA and threatened with death, if they did not cooperate. Coulson's Team thwarted this plot in the Battle at Cybertek, freeing the hostages, including Mrs. Zeller and Ace Peterson.
A New Beginning
Nick Fury decided that S.H.I.E.L.D., as is, was over. He told Captain America that he was leaving to find HYDRA in Europe. Later, he abdicated his position as director to Phil Coulson and gave him the Toolbox to find the Playground, a new base of operations. From there, they continued to fight HYDRA.
Some agents decided not to become a part of the new S.H.I.E.L.D. Phil Coulson was creating. Sharon Carter opted to join the CIA; Maria Hill became a member of Stark Industries in order to avoid legal persecution. Hill did meet with Coulson and attempted to have him join her to no avail.
Meanwhile, Robert Gonzales organized many other agents to join him in his version of the rebuilt S.H.I.E.L.D. Among those recruited were Bobbi Morse, Alphonso Mackenzie, Isabelle Hartley, and Anne Weaver. Once he learned of Coulson's organization, Gonzales sent Morse, Mackenzie, and Hartley to retrieve the Toolbox from Coulson, not knowing that Nick Fury was alive and had sanctioned Coulson's faction.
Many agents in the United States went into hiding to avoid persecution, such as Kara Palamas. Though Coulson attempted to find her, HYDRA got to her first, causing Coulson to believe that the two organizations were recruiting from the same pool of candidates. He was more successful with others such as Noelle Walters and her team, stationed in the Netherlands.
- "When I got out of the hospital it turned out there had never been a S.H.I.E.L.D., just HYDRA hiding behind one. I signed up to protect the world from these dangerous alien elements."
"We still do that."
"The hell you do, you use them, unleash them, you've got those freaks working for you."
- ―Felix Blake and Phil Coulson[src]
Despite Phil Coulson's efforts to rebuild S.H.I.E.L.D. and continue their goals, not all agents could look past HYDRA's deception. Felix Blake was disgusted by what the HYDRA Uprising had done so he refused to return to S.H.I.E.L.D. and instead created the Watchdogs, a team of radicals dedicated to hunting down and killing any and all Inhumans. Blake made a deal with R. Giyera to gain more weapons, unaware that Giyera was working for HYDRA's ancient Inhuman leader Hive.
- Captain America: The First Avenger
- Captain America: The Winter Soldier
- Agents of S.H.I.E.L.D.: 7.03: Alien Commies from the Future!
- Agents of S.H.I.E.L.D.: 7.04: Out of the Past
- Iron Man
- The Incredible Hulk
- The Avengers
- Marvel One-Shot: The Consultant
- Iron Man 2
- Marvel One-Shot: Item 47
- Avengers: Age of Ultron
- Agents of S.H.I.E.L.D.: 1.01: Pilot
- Agents of S.H.I.E.L.D.: 1.16: End of the Beginning
- Agents of S.H.I.E.L.D.: 1.17: Turn, Turn, Turn
- Agents of S.H.I.E.L.D.: 1.18: Providence
- Agents of S.H.I.E.L.D.: 2.14: Love in the Time of HYDRA
- Agents of S.H.I.E.L.D.: 2.03: Making Friends and Influencing People
- Agents of S.H.I.E.L.D.: 2.15: One Door Closes
- Agents of S.H.I.E.L.D.: 1.19: The Only Light in the Darkness
- Agents of S.H.I.E.L.D.: 1.20: Nothing Personal
- Agents of S.H.I.E.L.D.: 1.22: Beginning of the End
- Agents of S.H.I.E.L.D.: 2.19: The Dirty Half Dozen
- Agents of S.H.I.E.L.D.: 2.21: S.O.S. Part One
- Agents of S.H.I.E.L.D.: 2.05: A Hen in the Wolf House
- Agents of S.H.I.E.L.D.: 2.06: A Fractured House
- Agents of S.H.I.E.L.D.: 3.14: Watchdogs