- —Steven Rogers[src]
When the sentient Cosmic Cube named Kobik first came into existence by the hand of S.H.I.E.L.D. and manifested in the form of a scared child, it used her power of omnipresence to secretly seek the clone of the original Red Skull. The Red Skull once had in his possession a Cosmic Cube that was eventually shattered by Captain America. When S.H.I.E.L.D. used one of its fragments to create Kobik, its connection with the Red Skull passed on to Kobik. The Red Skull took advantage of Kobik's naivety to indoctrinate her in the ways of Hydra behind S.H.I.E.L.D.'s back. The Red Skull then executed his greatest scheme, and had Kobik turn Captain America into the best version of himself, which for Kobik, entailed he had to be loyal to Hydra.
In this new timeline, the young Steve Rogers first came into contact with Hydra when he was six years old in 1926,[note 1] after his mother Sarah was introduced by high-ranking member Elisa Sinclair into a local community run by Hydra. When Elisa had Sarah's abusive husband Joseph murdered, Sarah attempted to leave with Steve. Elisa confronted her before she had the chance, and Sarah seemingly died in the ensuing skirmish when she hit her head. Steve was then abducted to a Hydra training facility called The Keep. Elisa vouched for him, claiming he was the one they had been looking for.
Due to Steve's strong will, Hydra's earliest efforts at indoctrination failed. Because of this, he was regularly placed in solitary confinement and forced to watch reeducation films. In spite of his considerable academic abilities, Steve's poor physical condition and proneness to illness caused him to be rejected by both his instructors, namely Dr. Fenhoff, and his peers. In 1934, during one of Steve's many attempts to escape from The Keep, he was convinced to stay by Daniel Whitehall, the Kraken, who encouraged Steve to prove himself and embrace Hydra's beliefs, to value collectivism over individualism and to pursue the leadership of the strong. A year went by, and Dr. Fenhoff became to accept Steve due to his exhibition of leadership and dedication to Hydra's cause. Steve additionally met who would become his best and only friend, Helmut Zemo.
In 1936, when WWII was about to break out, Hydra decided to ally themselves with Adolf Hitler's Nazi Party with the intention to manipulate them to their advantage. In 1940, Steve returned to the United States on a mission to infiltrate the Army and kill Abraham Erskine, the lead scientist behind the Allies' Project Rebirth. After being rejected numerous times, Steve resorted to working at a diner Erskine frequented, with the objective to poison him. Steve caught Erskine's attention when General Chester Phillips recognized him from his many attempts to enlist, and praised his determination to serve the war efforts. Before Steve could poison Erskine, he was distracted by a robber. Steve attempted to stop him but failed miserably and got beaten up. This show of courage prompted Erskine to choose Steve as the subject for Project Rebirth's Super-Soldier Serum.
When Erskine invited Rogers for dinner, Steve took the chance and attempted to shoot him. Erskine almost convinced Steve to put down the gun, so Helmut, who had been working as Steve's handler during the mission, finished the deed. Using a device created by Fenhoff, Zemo extracted all of Erskine's knowledge from his mind. Due to how far into the project they were, the Allies brokered a deal with captured Hydra scientist Arnim Zola to carry on Erskine's work. However, Zola remained secretly loyal to Hydra.
Becoming Captain America
Steve was then elevated to the peak of human physique by Project Rebirth, and by 1942, he joined the Allies' war efforts as Captain America. Of course, Steve remained loyal to Hydra and acted as a spy, passing on to Hydra intelligence about troop deployments, supply routes and even a new mysterious super-weapon. In 1944, an attack of the Invaders on Hydra resulted in the imprisonment of Helmut and the death of his father and Hydra's leader Baron Heinrich Zemo. Steve tracked down Elisa with the intention to kill her on orders from Hydra, who believed she was the traitor that provided the Allies with intel on the Zemos' activity. Elisa pointed Steve to Nazi leader the Red Skull, whose machinations, including the death of Heinrich Zemo, allowed him to take control of Hydra and effectively subsume it into the Nazi party. Over the course of the following year, Captain America chased the Red Skull until finally confronting him in Berlin. Using Zemo as leverage, the Red Skull forced Steve to pledge loyalty to him. Frustrated and disheartened, Steve set out to leave the war until Elisa informed him about the Allies' new super-weapon, a Cosmic Cube.
In order to lift his spirits for a final mission, Elisa brought Steve back to the Keep where he was reunited with his mother, whose head injury had kept her from reuniting with Steve all these years. In preparation for the mission, Elisa warned Steve about the reality-warping properties of the Cosmic Cube, revealing the Allies planned to use it change reality so they won the war. Elisa ensured with her powers of clairvoyance that Steve would survive the change and wake up decades later in the changed world, tasking him with the mission to restore the world as it was. After stealing the plans for the Allied drone rocket that killed Baron Zemo and freeing Helmut, Captain America traveled to the ancient city of Ashomia in Japan, where he encountered the Kraken, as well as Isaac Newton and Nostradamus. The latter revealed Steve what his future held, and the chain of events that would allow for his return in this changed reality. When the Allies' use of the Cosmic Cube was sensed, Steve jumped into Nostradamus' pond to shield himself from the reality-warping.
In this way reality was changed into one where Hydra didn't win WWII, and Steve Rogers never served Hydra. While genuinely fighting alongside the Allies, Captain America would become frozen in ice, and was awakened in the 21st Century by the superhero team known as the Avengers, subsequently joining their ranks. In truth, this is the way events naturally occurred, until Kobik made it so it could be believed the timeline she fabricated, in which Captain America served Hydra, was the original.
Arrival to the Present
During a battle against the Iron Nail, Captain America had the Super-Soldier Serum within his body neutralized, which caused him to immediately age into an elderly. Later on, the clone of the Red Skull had Hydra double-agent Erik Selvig propose to S.H.I.E.L.D. to use Kobik's reality-warping powers to create a prison for supervillains, where each inmate would be turned into a mild-mannered citizen. The Red Skull's further machinations led to a supervillain revolt breaking out when Steve was visiting Pleasant Hill. In the middle of the crisis, Rogers was almost killed by Crossbones. Kobik took pity on Steve, and decided to return him to his prime. While it seemed like Steve was simply back in shape, in reality Kobik had the Steve from her timeline supplant him.
Unbeknownst to the Red Skull, even though Rogers reported to him, he was actually despised by Steve. Believing that the Red Skull's vision of Hydra preached blind hatred and intolerance with the purpose to glorify himself, Captain America even set out to kill him in order to restore Hydra's former glory. When ordered by the Red Skull to kill Baron Zemo and Erik Selvig, Rogers secretly kept both of them alive. While Steve convinced Selvig to work for him right off the bat, he kept Zemo prisoner, and talked him into eventually believing that his version of history was the original and that it had to be restored.
Both the Red Skull and Rogers had to halt their operations in light of the appearance of an Inhuman with the ability to predict the future named Ulysses Cain. In order to test Ulysses' abilities and see if the emergence of more pressing threats for him to predict could be used to conceal his own schemes, Rogers planted the seeds that led to Bruce Banner being killed over a prediction, which in turn caused the friction between Iron Man and Captain Marvel to escalate into a war that split the superhero community. In a turn of events, Captain America became the protagonist of another of Ulysses' visions, in which he was killed by Spider-Man in the steps of the Capitol Building. Captain America joined Spider-Man in Washington, D.C. to prove the vision wrong, and witnessed the final battle between Iron Man and Captain Marvel. Ulysses' vision involving him even invigorated Rogers' conviction. Even though the vision did show him dying at Spider-Man's hands, he managed to catch a glimpse of the scenario surrounding his supposed death, that of an America under Hydra's rule.
Under the orders of the Red Skull, Captain America secured alien eggs containing Chitauri queens. The presence of the eggs on Earth combined with their instincts and simple-mindedness prompted waves of these aliens to regularly attempt to swarm the planet to get to them, with each wave growing in size and frequency. The Red Skull's endgame was to have these aliens eventually overwhelm and destabilize the Earth.
Taking advantage of the resurgence of the Red Skull's Hydra, Captain America supported Sharon Carter in proposing to the Senate the creation of a bill known as the "S.H.I.E.L.D. Act." to expand the organization's power. Not long after that, S.H.I.E.L.D. Director Maria Hill faced a tribunal to determine the future of her career due to numerous controversial decisions, namely the creation of Pleasant Hill. After Hill presented the plans of the impenetrable Planetary Defense Shield in an attempt to sway the tribunal of the World Security Council in her favor, Captain America orchestrated the death of tribunal member Charles Dalton to ensure Hill was found guilty and fired. Hill went on the run and handed over the plans for the Planetary Defense Shield to the Alpha Flight Space Program. Because the creation of the Shield could've compromised the success of the Chitauri wave, Rogers attempted to talk Alpha Flight Commander Captain Marvel out of building it. Carol still endorsed its creation to the President of the United States, and secured the construction of its generator. Having failed to halt the Shield's creation, Steve had his ally and hacker Rick Jones hack into its security systems, and later on send Steve its access codes.
Captain America suggested Carter to replace Hill, but Sharon herself declined the offer and postulated Steve. Rogers' assumption of the Director's chair coincided with the S.H.I.E.L.D. Act being signed into law with bipartisan support in Congress. The S.H.I.E.L.D. Act drastically expanded S.H.I.E.L.D.'s authority within the United States in areas concerned with law enforcement, mass surveillance, and resource allocation, also enabling the organization to become the de facto "top cop" in an event of a national state of emergency. It even allowed, in case of national emergency, for the director of S.H.I.E.L.D. to take absolute control of the country.
Once Baron Zemo was on Rogers' side, he began to rally all of the supervillains that were inmates in Pleasant Hill, assembling an Army of Evil. Additionally, Elisa Sinclair somehow resurfaced as the new Madame Hydra, and began to gather powerful allies to serve as Captain America's High Council of Hydra. Following his defeat at the hands of the Avengers Unity Division, the Red Skull had the portion of Charles Xavier's brain that he had previously grafted into his own cranium surgically extracted. Rogers orchestrated Red Skull's escape from custody solely so he could kill him himself, now that the Skull lacked the telepathic abilities Charles Xavier's brain granted him. Once the Red Skull was dead, Rogers consolidated power as the new Hydra Supreme, and reunited with Sinclair.
After taking over the Thunderbolts and seemingly killing the Winter Soldier, Baron Zemo secured Kobik. However, her humanoid form was destroyed in the process, leaving behind Cosmic Cube shards. Before the Cube could be reassembled and used to change the world to match Rogers' timeline, Selvig had a change of heart and teleported the shards away, scattering them all over the world, before killing himself. Even though the plan consisted of taking over the world and reshaping it, Madame Hydra encouraged Steve to carry on with the first part.
Two new crises were set up coordinately with the imminent arrival of a Chitauri wave of trillions of aliens: the Army of Evil's attack on Manhattan and the S.H.I.E.L.D. Helicarrier Crescent dropping off the radar. Each of these crises were orchestrated to neutralize key elements in America's defense. The crew of Crescent had been brainwashed by Doctor Faustus, and establishing contact with S.H.I.E.L.D. allowed for his hypnotic message to spread out to the organization's entire fleet; the Chitauri invasion required the heavy hitters of the superhero community to hold them off in orbit, and Rogers subsequently sealed them off with the Planetary Defense Shield; and finally, the Army of Evil's attack served the purpose to lure countless of the nation's heroes to Manhattan, so they could be enclosed in a dome of Darkforce by Blackout. The state of emergency additionally had put into action the effects of the S.H.I.E.L.D. Act, legally putting the government and military in Captain America's hands. With these strikes dealt, Captain America mobilized S.H.I.E.L.D.'s entire fleet to take over Washington, D.C. and consolidate power over the country. A contingent of America's remaining heroes who hadn't been neutralized attempted to stop the takeover, but were swiftly defeated.
After some time had passed since Hydra's conquest, the people of the United States were getting accustomed to their new fascist regime, mainly due to the use of mind-altering substances in water supplies to increase docility and receptiveness. Mutants had been displaced to the sovereign land of New Tian and Inhumans were being held captive in detention facilities. A handful of heroes that hadn't become exiled formed the Underground, an alliance of super-powered and civilian rebels led by Hawkeye stationed in The Mount in Nevada, and others under Hydra's influence joined Hydra's own Avengers.
Following an increment of Underground activity in the area, the High Council pressured Captain America into laying siege to Las Vegas. Steve gave Madame Hydra the power to do carry out the attack as he was uncertain, and she did. Disgruntled by this event, Rogers set out to find the Cosmic Cube shards to reshape the world as soon as possible. Hydra proceeded to race the Underground to find the fragments, as the rebels had learned of their existence and hoped to use them to return Captain America to normalcy. Hydra eventually acquired most of the fragments, and even raided the Underground's base to retrieve the only two shards they had collected. This victory was not without a cost, as Madame Hydra sacrificed herself to protect Rogers from the detonation of The Mount.
Another insurgent group, called the Red Room, which was led by Black Widow and had Spider-Man among its ranks, attacked Captain America during a ceremony at the Capitol Building. Black Widow had set out to kill Captain America in part to prevent Ulysses Cain's vision from being fulfilled, which entailed Spider-Man becoming a murderer. When her attempt to keep Spider-Man at bay failed and the young hero confronted Captain America in an effort to stop running from his supposed fate, Black Widow tried to break up the fight, which resulted in her death when she was fatally struck by Rogers' shield. Natasha's death caused Steve's dismay to grow stronger, as it added to the unwilling casualties of his crusade. Because of this, Rogers became determined to assemble the entirety of the Cosmic Cube, and take action to acquire two fragments that evaded him, those possessed by Black Panther in Wakanda and by Emma Frost in New Tian, respectively. Hydra went to war against these nations, capturing T'Challa and forcing Frost to surrender.
At the same time, the Underground gained a second wind when they came across the final Cube shard, and used its residual reality-warping powers to influence the events that saw the Darkforce dome brought down and the Planetary Defense Shield destroyed. United at last, a contingent consisting of almost every single hero mounted an attack on Washington, D.C. which proved to be successful. Even though Hydra's forces were decimated, the Hydra Supreme confronted the heroes using a suit of armor that granted him the power of the fragments in his possession, which was enough to allow him to reshape reality in Hydra's image. Sam Wilson handed over the final fragment to Steve, and he proceeded to merge the Cube back together. However, with Ant-Man's help, the Winter Soldier subatomically infiltrated the Cube as Rogers was assembling it. This act allowed Bucky to reach into Kobik's mindspace and bring out both her and the real Steve Rogers, who materialized in front of his fascist counterpart. After Kobik undid the changes to reality caused by the Hydra Supreme, the two Captain Americas battled. Following an arduous fight, the Hydra loyalist Steve Rogers was defeated. The heroes stood victorious, and in the course of the following weeks, the United States returned to normalcy.
After the Empire
The Hydra Supreme Steve Rogers was subsequently imprisoned in a high-security facility called the Shadow Pillar, but secretly had at least one Hydra loyalist as a guard. During his imprisonment, Rogers was visited by Deadpool, one of the handful of heroes that he had manipulated into serving Hydra. Since his life was turned upside down as a consequence of Hydra's regime, Deadpool blamed Rogers for it. However, Deadpool left Rogers' cell almost as quickly as he infiltrated it, leaving with the promise to take something from him whenever he visited him.
The Supreme Commander's first attempt at a break out came by the hand of Baron Zemo, who had kept Hydra running following Rogers' fall. The escape was intercepted by another vigilante who had been manipulated by Rogers, the Punisher, who had stolen the War Machine Armor and planned to use it against Hydra. The Punisher took down the helicopter Hydra was using to escape and defeated Baron Zemo. After the authorities arrived, Rogers was again apprehended.
Imprisoned once more, Rogers ultimately received a pardon by the President of the United States through means of the Power Elite, who had began feeding a disinformation campaign to lead the public to believe that Captain America was actually the Supreme Leader all along, lining up with Rogers' arrest for the alleged murder of Thaddeus Ross. As he was leaving the Shadow Pillar with Alexa Lukin, Selene ambushed him, breaking his leg and melting his body. The Supreme Leader groaned in pain trying to recite Hydra's mantra in a pool of his own blood, as his body burst into flames.
- The panel of him saying "Hail Hydra" became a popular internet meme.
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