Hydra is a world-wide criminal organization dedicated to global domination, with the intended goal of establishing a totalitarian fascist "New World Order". Over the years, Hydra secretly infiltrated S.H.I.E.L.D. and used the agency to their advantage in many ways. They subverted a large proportion of its agents, and silently killed off anyone who got in their way.
Dawn of TimeEdit
The members of the Hydra cult believe that it's Hives destiny to become ruler of Earth and Hive would reward those that rescued him with power.
Over the centuries Hydra has had many names and appearances, but what every group had in common was that they all sacrificed people to the Monolith. The members of Hydra knew Hive needs a human host to inhabit in order to live thus, every few decades, one of the heads of Hydra would be randomly selected to go through the Monolith portal to Maveth where Hive would kill them and use their body as his new vessel.
Since at least 1839, Hydra would choose the sacrifice through the stone ceremony; a white stone is placed into a bag with several black stones, each Hydra head must reach into the the bag to pull out a stone, and whoever drew the white stone becomes Hive's new host.
World War IIEdit
According to Malick, the Red Skull wasn't a member of the Hydra cult, but rather founded his version of Hydra on the same principle that "the ultimate power was not of this world."
Hydra was the scientific research branch of Adolf Hitler's Third Reich, but, after discovering the Tesseract, Johann Shmidt, the Red Skull and leader of Hydra, decided that Hydra could grow no further under Hitler's regime and no longer shared the Nazis goal of creating a master race. Hydra then became a separate organization with the goal of world domination.
Using the Tesseract's energy, Hydra scientist invented new weapons of war. Schmidt's final plan was to lead a series of strategic bombings against major American cities including Boston, Chicago, and New York City.
However, thanks to the sacrifice of Captain America, the Red Skull was killed and his plan for world domination was thwarted.
The S.S.R. destroyed any remaining Hydra bases and arrested anyone still loyal to Hydra, but, unknown to the world, Hydra was still a functioning organization and had only been driven into hiding.
S.H.I.E.L.D is HydraEdit
Since its founding, S.H.I.E.L.D had been influenced by Hydra. Arnim Zola, a Hydra scientist, was recruited by S.H.I.E.L.D following the end of WWII as part of Operation: Paperclip. While working for S.H.I.E.L.D, Zola was also working to rebuild Hydra from inside the agency with missions such as the assassination of Howard Stark, Iron Man's father.
In Captain America: The Winter Soldier, after decades in hiding, Hydra was going to finally fulfill its goal of world domination by using S.H.I.E.L.D.'s Project Insight. Zola wrote an algorithm designed to analyze peoples digital history (their financial records, medical history, social media content, voting habits, etc.) and then use that information to predict whether that person is a current threat to Hydra or will be a threat in the future. After the targets are selected, the Insight helicarriers eliminate them, a few million people at a time according to Sitwell.
After Director Fury grew close to learning of Hydra's plan, Hydra sent a team of agents with the Winter Soldier to assassinate him and frame Captain America for Fury's murder. Fury survived the assassination attempt, but decided to fake his death and go into hiding.
As soon as the Insight helicarriers launched, Hydra sent out an encrypted message across all S.H.I.E.L.D. communication channels that read "out of the shadows into the light, Hydra" which was a signal for all Hydra sleeper agents within S.H.I.E.L.D. to activate. Hydra was intent on killing every S.H.I.E.L.D. agent and taking control of every S.H.I.E.L.D. facility in the world.
However, Captain America, Black Widow, and Falcon were able to reprogram the three Insight helicarriers to target each other and thereby destroy each other, thus thwarting Hydra's plan for world domination.
The War Continues Edit
Hydra had effectively destroyed S.H.I.E.L.D., but, even with the organization gone, Agent Coulson's team continued their personal fight against Hydra. Coulson killed Garret and stopped his plan to create an army of Deathlock super-soldiers. Also, they killed Dr. Whitehall, another head of Hydra, who wanted to use the power of the Diviner to achieve world domination.
In "A Hen in the Wolf House," Whitehall tests a kind of poison he invented that mimics the effects of the Diviner on humans at a wedding party by poisoning the champagne with it. The poison killed eight people, six were naval officers that were part of an anti-Hydra unit.
In "A Fractured House," Senator Christian Ward gives a speech at the United Nations saying how S.H.I.E.L.D. and Hydra are not the same thing and how they need to put more effort into destroying Hydra. Christian also publicly confesses that his little brother Grant Ward is an agent of Hydra and he'll make sure Grant is punished for his crimes.
In "Aftershocks," after Dr. Whitehall is killed by Coulson, the remaining heads of Hydra have a meeting where they decide that whoever destroys S.H.I.E.L.D. will be rewarded with the honor of replacing Whitehall as Hydra's new head.
S.H.I.E.L.D. dealt a major wound to Hydra when they tricked one of the heads of Hydra, Mr. Bloom, into killing three of the other heads, specifically the Banker, the Baroness, and the Sheikh. Coulson had Hunter go undercover as a Hydra agent and then convince Bakshi, who believed he had just escaped from S.H.I.E.L.D. custody, into believing the other Hydra heads wanted to kill Bloom. Afterwards, Hunter and Bobbi stormed Bloom's estate, killed him too, and captured Bakshi.
In "The Dirty Half Dozen," Coulson's team infiltrates a Hydra base in the arctic where Hydra has been experimenting on powered people. After freeing Hydra's prisoners, they disable the bases missile defense system thereby allowing a large S.H.I.E.L.D. strike force to destroy the base.
After Agent 33 is killed, Ward blames Coulson and S.H.I.E.L.D. for her death and begins to rebuild Hydra for the purpose of using it as a means to take his revenge. Ward starts recruiting former Hydra agents to his version of Hydra, telling them he wants to rebuild Hydra stronger than it was before, and that he's Hydra's new head.
Hive's Return Edit
With the world-wide terrigen outbreak causing inhumans all over the world to spontaneously go through terrigenesis, Gideon Malick, a member of the Hydra cult and one of Hydra's heads, forms the A.T.C.U. with the purpose of collecting inhumans for Hive to control when he returns to Earth.
When Malick learns Coulson was able to bring Simmons back from Maveth through the Monolith, he abducts both Fitz and Simmons and forces them to tell him how they brought Simmons back. Fitz explains to Malick how to calculate when and where the portal will open next on Maveth. Malick then sends a team of Hydra agents being led by Ward through the Monolith portal with the mission of finding Hive and bringing him back to Earth.
In "Maveth," Malick accomplishes what Hydra has been trying to do for thousands of years, return Hive to Earth.
In "Paradise Lost," Hive calls a meeting with the other members of the Hydra cult at Malick's mansion where he proves his power to them by revealing his true form.
In "The Team," The Secret Warriors (Daisy, Lincoln, Joey, and Elena) rescue May and the others from a Hydra base and capture Malick as well. Coulson interrogates Malick and Malick explains to Coulson how Hive killed his daughter, Stephanie. Malick then betrays Hydra by telling Coulson all he knows about the organization. Daisy, later, kills Malick while being controlled by Hive.
Using the information Malick gave them, Coulson works with Talbot to coordinate attacks on several Hydra facilities around the world, effectively destroying the organization.
In "The Patriot," a team of former Hydra agents, turned mercenaries, tries to assassinate Director Mace, but S.H.I.E.L.D. defeats them.
- Hydra agents within S.H.I.E.L.D. would communicate with each other through the white noise existing between the gaps in S.H.I.E.L.D. communication channels.
- Dr. Whitehall, one of the heads of Hydra, often resorted to brainwashing in order to force people like Donnie Gill and Agent 33 into joining Hydra. Ward explained to Daisy that Hydra rarely resorts to brainwashing as a means of coercion as some people aren't susceptible to it and it's a long and difficult process. Brainwashing is mostly reserved for high-valued targets.
- A Hydra in Greek mythology was a creature where, if you cut off a head, two more would take its place, and this is why the Hydra phrase is, "Cut off one head, two more shall take its place". Heracles (Hercules in Roman Mythology) faced the Lernean Hydra in his Second Labor, burning the neck stumps to prevent this regrowth.