Rising out of the fall of the Axis Powers in World War II, HYDRA was apparently created as a secret organization for global domination by Nazi spymaster Baron Wolfgang von Strucker along with Kraken. This developed with the help of an alliance with Shoji Soma, grandmaster of the Hand. When the power base pf HYDRA felt firmly established, Strucker installed himself as its supreme commander and ended the alliance with the Hand.
HYDRA recruited from the remnants of the Nazi's military forces and acquired alien technologies to advance its resources beyond those that most governments possessed. Strucker chose to build HYDRA"s forces quietly over the following decades.
Hydra was created by Stan Lee and Jack Kirby.
Through the decades, HYDRA was consistently used as a source of all-purpose terrorism and villainous cannon fodder with its legions of uniformed operatives and its philosophy "cut off one head and two will take its place." It also consistently served as an opposite number for S.H.I.E.L.D., Marvel's source of all-purpose espionage and heroic cannon fodder.
A number of other criminal organizations began as branches of HYDRA before striking off as their own independent entities, such as A.I.M., with its own various factions, and separate incarnations of the Secret Empire.
Baron Von Strucker has most commonly depicted as HYDRA's "Supreme Hydra." However, the organization fractured after his first death, leading to a variety of HYDRAs with an inconsistent hierarchy of leadership. This continued even after Strucker was resurrected and he supposedly reunited HYDRA. Others claiming the title of Supreme Hydra have included Viper and the Gorgon.
This was addressed in Secret Warriors by Jonathan Hickman, who introduced the HYDRA High Council. This embraced the sometimes inconsistent portrayals of HYDRA by rationalizing it as HYDRA now having a council-based leadership that including Von Strucker, Viper, Gorgon, the Hive, Kraken and a new Madame Hydra. The structure of HYDRA was much more strongly defined through the course of this series but also heavily changed in the end due to an internal civil war. Much of the High Council was left either dead or defected, leaving HYDRA under the command of Gorgon and Madame HYDRA. The end of this series also revealed the role of Von Strucker's arch-foe, Nick Fury, in the birth of the organization.
Additionally, an extradimensional rift has allowed agents of HYDRA from an alternate Earth to appear on Earth-616. This version of the organization is firmly under the command of Queen Hydra.
Major Story Arcs
Enemy of the State
For further information: Enemy of the State
In an alliance between HYDRA and the Hand, Baron Von Strucker orchestrated a plan that saw Wolverine taken and killed by the Gorgon. Wolverine was then resurrected by the Hand's magic as a loyal agent of HYDRA. Wolverine was then sent on a killing spree in the superhuman and law enforcement communities in the service of HYDRA. Some of these superhumans were made into HYDRA agents using the same Hand magic that was used on Wolverine. Along the way, he also acquired defense secrets and Reed Richards' technology for HYDRA. He was eventually brought down by a combined effort from the superhero community and freed of HYDRA's brainwashing. Despite this, HYDRA still accomplished a great deal.
All was not well within HYDRA, though. The Gorgon had entered into an affair with Elsbeth Von Strucker, Baron Von Strucker's wife, and used this to depose him as the Supreme Hydra. Both HYDRA and the Hand were now under the Gorgon's command, and he focused on the part of Von Strucker's plan involving using the Hand's magic to recruit superhumans. He ordered the mass murder of both superheroes and supervillains alike so that their bodies could be revived as loyal HYDRA agents, quickly gathering together a small army.
However, S.H.I.E.L.D. had successfully deprogrammed Wolverine, and the mutant now wanted nothing but revenge. He tore through the Hand and Gorgon's former death cult, the Dawn of the White Light. He then came after Gorgon as he was carrying out a plan to assassinate Nick Fury. It was only Wolverine's last second intervention that prevented Gorgon from killing Fury, and Wolverine just barely managed to kill Gorgon, cutting off another head of HYDRA.
The Seven Capital Cities of Heaven
A man known simply as Xao formed an alliance with HYDRA in a plot to break through the mystical barrier separating Earth from K'un-Lun and pillage the city of its ancient wonders. This plan failed when Iron Fist managed to unite the Immortal Weapons of all the other cities of Heaven against HYDRA's invasion force. The never made it through to K'un-Lun, and Xao was killed.
Nick Fury: Agent of Nothing
For further information: Nick Fury: Agent of Nothing, Secret Invasion
When Nick Fury went rogue from S.H.I.E.L.D. and the government, it was discovered that for many years HYDRA had one of its tentacles into the highest levels of S.H.I.E.L.D., effectively meaning Fury had been working for HYDRA all this time. Ironically, HYDRA was dealing with its own infiltrators around the same time, namely the Skrulls. Upon realization that he had been breached by the Skrulls, Strucker chose to completely destroyed his undersea base codenamed Ichor with all of its personnel. He then reconvened HYDRA at Gehenna, their most treasured stronghold, and called the full HYDRA High Council together. They even forced the Grandmaster of the Hand to resurrect the Gorgon to convene the full council of HYDRA's leaders.
So it was that Baron Strucker, Kraken, the Hive, the Gorgon, Madame Hydra and the Viper all met together for what was apparently the first time, and Strucker laid out his intentions. Fury had discovered their true structure and was going to come for them. Rather than wait, he wanted HYDRA to go to war with Fury. Though some were reluctant, there was unanimous consent for Strucker's war.
Wake the Beast
For further information: Wake the Beast
HYDRA was betrayed by one of its leaders Madame Hydra, actually Contessa Allegro de la Fontaine. She was, in fact, a sleeper agent of Leviathan, an ancient enemy of HYDRA's dating back to the years of its very formation. She acquired from them an alien power source that could be used to awaken Leviathan's leader from stasis, and so rose Orion, leader of Leviathan. The two organizations met for what HYDRA hoped could be an understanding between them. Leviathan was not interested in any understanding, and so fierce war began between Leviathan and HYDRA.
All the while, Nick Fury and his small force of Secret Warriors manipulated events to urge them on.
Wheels Within Wheels
HYDRA took heavy losses in the war with Leviathan, and this was made worse when Nick Fury and his Secret Warriors successfully destroyed Gehenna. The loss of this stronghold fractured HYDRA's leadership, and two factions clashed in an internal civil war. One side rallied behind the Gorgon and the other behind Kraken. This only increased HYDRA's losses, and it turned out this was all carefully orchestrated by Nick Fury. Kraken was not the original man who helped create HYDRA but was actually Jake Fury. HYDRA had been played into killing itself, and Nick Fury personally executed Strucker.
Though diminished, HYDRA managed to endure because Fury had not accounted in his plans for Gorgon's resurrection. What remained of HYDRA gathered un his and Viper's leadership.
Spider-Man saved Tony Stark from an attack by HYDRA. Jameson recalls this events after Spidey's death.
They are well underway with their plan to take over the world. This version is being led by Madame Hydra (Sue Storm) and her lover, Wolverine. Various other superhumans, including Captain America (now Captain Hydra), Iron Man and Slaymaster, are agents of HYDRA in this world. One of the Exiles' foe, the original character Venger later becomes an agent of HYDRA, as well as Boy-Bob Banner.
A terrorist organization that was involved in Cold War and battled against S.H.I.E.L.D. Colonel Gagarin was a member.
Nick Fury: Agent of S.H.I.E.L.D.
They seem more like a Men-In-Black team.
Avengers: Earth's Mightiest Heroes
For further information: Avengers: Earth's Mightiest Heroes
In the continuity of this Disney XD animated series, HYDRA serves as a stand-in for the Nazi's in World War II and features prominently in Captain America's adventures in that era with Baron Heinrich Zemo and the Red Skull as its high-ranking commanders. HYDRA persists as a recurring threat through the first season in modern day as well under the command of Baron Von Strucker, though Viper is also present as Madame Hydra. Grim Reaper plays the role of one of HYDRA's foremost superhuman operatives, and Black Widow seemingly betrays S.H.I.E.L.D. to join them, secretly doing so as a double agent for Nick Fury.
HYDRA is ultimately defeated later in the first season when it goes with war with A.I.M. over possession of the Cosmic Cube. The Avengers intervene, leading to a battle between Captain America and Baron Strucker for the cube. They both touch it, seemingly having no affect. Both HYDRA and A.I.M. are then defeated and incarcerated.
HYDRA is the major villain in the rare video game titled Spider-man: Web of Fire
In Marvel Ultimate Alliance 2, one of the levels includes an old HYDRA base that the Anti-Registration group was using. HYDRA's aerial base can be seen attacking the S.H.I.E.L.D. Helicarrier in the latter's stage in Marvel Capcom 3 and the organization's logo can also be seen on the car that attempts to run She-Hulk down in one of her special moves.
Ultimate Avengers 2
Some HYDRA agents appear at the beginning fighting against Cap. After Cap defeats most of the agents, two of them try to escape in a van. Cap throws his shield, which slices clean through the van back-to-front, and causing it to skid out of control. The van crashes into a tank of some sort of chemicals, which then burst open, showering the van. The van melts along with both HYDRA agents.
X-men: The Official Game
HYDRA is partially responsible for the creation of the Master Mold and Sentinels alongside William Stryker. Under orders of their leader, Silver Samurai, HYDRA infiltrates Stryker's base to remove all evidence and Sentinel equipment, and by accident, activated the Master Mold. Lady Deathstrike was an agent of HYDRA too.
Captain America: the First Avenger (2011)
For further information: Captain America: the First Avenger
HYDRA is featured in this World War II era movie as a scientific research and development branch of the Third Reich. It is operated by the Red Skull and goes rogue from the German forces with its own advanced technology and weaponry. The organization is defeated after Captain America apparently kills Red Skull in battle, leading to their defeat by American forces. They appear in the movie's video game too.
For further information: X-Men: Evolution
In this X-Men animated series for Kids' WB, HYDRA appears briefly with seemingly Viper in command and as part of Wolverine's history. HYDRA is responsible for the creation of X.23 from Wolverine's cloned DNA. It is also implied that HYDRA was involved in the Weapon X project.