HYDRA Uprising

"We don't know how long HYDRA's been inside S.H.I.E.L.D. but they are taking control." "HYDRA? What? Where?" "Everywhere! Among us!"

- Anne Weaver and Jemma Simmons

The S.H.I.E.L.D. Civil War, also known as the HYDRA infiltration, was a major conflict that went back as early as the 1940s. After World War II, the security agency S.H.I.E.L.D. was founded, but was soon infiltrated by HYDRA, the rogue Nazi science group originally formed by the Red Skull prior to his disappearance.

For the next several decades, HYDRA grew within S.H.I.E.L.D.'s ranks, manipulating the agency 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.

Prelude
"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

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.

Secret War
"For 70 years HYDRA has been secretly feeding crisis. Reaping war. And when history did not cooperate, history was changed. HYDRA created a world so chaotic that humanity is finally ready to sacrifice its freedom to gain its security. Once the purification process is complete, HYDRA's New World Order will arise."

- Arnim Zola to Captain America and Black Widow

Shortly after the war, Dr. Zola was able to find James Buchanan Barnes, Captain America's teammate and Zola's former test subject, 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.

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 Howard 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 on 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's agents in S.H.I.E.L.D., eventually became one of the agency's directors, and a member of the World Security Council. Senator Stern served as HYDRA's mole inside the United States Senate.

Troubles in Washington
"S.H.I.E.L.D. is not what we thought it was. It's been taken over by HYDRA."

- Captain America

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 Earth. However, the leaders of HYDRA planned to use the Helicarriers to eliminate anyone who had been distinguished as a threat by 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 later, 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. Fury found out about the true purpose of Project Insight and used the Winter Soldier's attempt on his life to fake his own death. Recruiting Captain America, Black Widow, Falcon, and Maria Hill to his cause, he destroyed the insight Helicarriers and personally shot Pierce dead. 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.

The Battle of the Hub
"Phil, this is a battle for S.H.I.E.L.D.'s soul, and we're on the front lines. History will remember us this day." "That's right. It's for S.H.I.E.L.D.'s soul, and murder without consideration isn't..."

- John Garrett and Phil Coulson

Exposed, HYDRA immediately began covering their tracks, 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. Academy, their attempted takeover of the Hub was thwarted by Phil Coulson and his team. Coulson's efforts led to the capture of HYDRA operative John Garrett, who managed to escape with the death of Victoria Hand by Grant Ward.

In light of the new information, the governments that controlled S.H.I.E.L.D. 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.