HYDRA is a terrorist organization dating back to the time of World War II with the intention of taking over the world.
- Arnim Zola: Left to join Masters of Evil. Possibly killed by Amora.
- Baron Zemo: Left to join Masters of Evil. Captured and imprisoned in Prison 42.
- Black Widow: Actually a double agent for S.H.I.E.L.D. infiltrating the organization.
- Red Skull: Head of HYDRA during World War II. Unknown if he continued any ties in modern times.
In the 1940s, they overran Europe under the leadership of Baron Heinrich Zemo with the Red Skull as their super-soldier. Though at one point they were a branch, HYDRA had ambitions of replacing the Third Reich. Allied forces eventually defeated them.
One of HYDRA's attempts to win World War II involved taking mythological beasts from the realms of Asgard and using technology to enslave them, such as the Frost Giant Ymir, in an attempt thwarted by Captain America and Bucky.
In modern times, they were known to steal some of Stark Industries technology to bolster their plans for world domination. HYDRA agents attack the United Nations and fight Iron Man. HYDRA unleashes a HYDRA Octopus Robot to fight Iron Man. Iron Man defeats the last octo-bot when S.H.I.E.L.D. arrives. After Iron Man leaves, the S.H.I.E.L.D. agents arrest the HYDRA agents involved in the attack. The HYDRA agents are dropped off at the Vault where Nick Fury goes to interrogate Baron Strucker. During that time, it is shown that one of the HYDRA agents was actually Grim Reaper in disguise as part of a plot to spring Baron Strucker from prison. Both of them are defeated by Nick Fury and Baron Strucker is placed back in his cell while Grim Reaper is also locked into a cell of his own.
Baron Strucker and Grim Reaper are among the prisoners that escape from the Vault as they make their way back to HYDRA Island.
Zemo finds Strucker ruling HYDRA, then lets him keep it, seemingly severing ties with the organization.
Grim Reaper and HYDRA meet with MODOC and A.I.M. for a transaction that would help in the creation of the Cosmic Cube which is crashed by Hawkeye in his search for Black Widow. Grim Reaper manages to escape, not knowing that Hawkeye had placed a tracer on him, while the defeated HYDRA and A.I.M. agents were arrested by S.H.I.E.L.D. When Hawkeye, Mockingbird, Captain America, and Black Panther trace Grim Reaper to HYDRA Island, they end up fighting the forces of HYDRA. Baron Strucker ended up having the computer activate the self-destruct sequence upon telling it "Codename: Fenris." Though Hawkeye goes after Black Widow and Baron Strucker. Hawkeye is taken down by Black Widow who secretly attacks Baron Strucker as he tries to take Hawkeye's youth. Black Widow escapes from HYDRA Island with Baron Strucker while Grim Reaper, Madame Hydra, and the remaining HYDRA Agents present are arrested by S.H.I.E.L.D. While waiting for MODOC, Black Widow tells Baron Strucker that Black Panther attacked him from behind. MODOC arrives and tells Baron Strucker that the Cosmic Cube experiment was a failure and gives back the money. After MODOC left, Baron Strucker suspects that MODOC was lying about the Cosmic Cube experiment being a failure.
The organization dates back to ancient Egypt, the time of Apocalypse.