The HYDRA Uprising, also known as the HYDRA Infiltration and the Fall of S.H.I.E.L.D., 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 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 all of the undercover HYDRA agents had revealed themselves, the War on HYDRA began, letting the Avengers and the reformed S.H.I.E.L.D. fight HYDRA without being manipulated from the inside.
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, Dr. Zola was able to find James Buchanan Barnes, Captain America's best friend, 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. 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 operatives in S.H.I.E.L.D., eventually became one of the agency's directors, and a member of the World Security Council.