Kobik, a sentient
Cosmic Cube, rewrites reality, creating a new timeline where
Captain America is a
Hydra sleeper agent. This version of Rogers becomes the head of
S.H.I.E.L.D. and is appointed head of Earth's defense forces during a
Chitauri attack on Earth. As the shield around Earth is brought online, Rogers reveals his allegiance to Hydra as the
Hydra Supreme. Meanwhile, all of Manhattan is imprisoned in
Darkforce energy by
Blackout.
Iron Man sends a signal out to the other heroes to meet in
Washington, D.C. as fast as they can. Hacker
Rayshaun Lucas is entrusted with key data by
Rick Jones, which Rick states will prove the truth about Captain America. Rick and
Sharon Carter are captured by Hydra, but refuse to swear loyalty to them. Hydra Supreme executes Rick and dispatches
Helicarriers to raze Las Vegas. Hydra Supreme and
Madame Hydra resume their search for the Cosmic Cube to undo the Allies' victory in World War II. Having received and analyzed Rick's data, Iron Man determines that Cosmic Cube fragments have been scattered around the world and could return Rogers to his proper self if brought together.
Black Widow sets off to kill Rogers herself, reasoning that, even if Rick's theory is true, Rogers would prefer to die than be used in this manner. Hydra's forces discover a Cosmic Cube shard in
Atlantis, but learn that it is a decoy planted by
Namor. Hydra Supreme places Namor in a position that forces him to give Hydra Supreme access to the Cosmic Cube fragment in Atlantis. At the Hydra Helicarrier, it is revealed that Hydra has resurrected
Bruce Banner, but do not expect him to live for long. As the Hulk, Banner attacks Hydra's fortress and collapses the roof over Iron Man and Hydra Supreme as Hydra's resurrection process wears off. On the Hydra Helicarrier, Madame Hydra detects an unusual amount of energy in the Mount and rushes in. Madame Hydra arrives and teleports Hydra Supreme away at the last second as Iron Man explodes, destroying the base and killing Madame Hydra. The Red Skull tortures "Steve Rogers," claiming he is granting Rogers "peace."
Spider-Man and Black Widow are about to proceed with their mission to assassinate Hydra Supreme.
Punisher arrives right before Black Widow can take the shot and the two begin to fight. Black Widow fights her way through several Hydra guards, but is attacked and killed by an unknown assailant. Rogers then tackles the Red Skull and they both plummet off the cliff into the water below.
Maria Hill finds Blackout in prison and kills him, freeing Manhattan from the Darkforce dome. After emerging from the ocean with the remaining Cube fragment in his hand,
Sam Wilson meets up with the other heroes at the Triskelion. As the Underground plans to spring into action, they know that the battle is still in Hydra's favor with
Black Panther still a captive and Hydra Supreme having most of the Cosmic Cube fragments. Hydra Supreme uses a version of
Iron Man's armor to harness the Cosmic Cube. Meanwhile, Kobik learns that the original Steve Rogers still exists inside Kobik's mental world and restores his memories. Hydra Supreme absorbs the final Cube fragment into his armor, but is thwarted by
Winter Soldier and
Ant-Man. Rogers convinces Kobik to stand up and fight back, then escapes to the real world. Hydra Supreme is taken to a high-security prison known as Shadow Pillar, where he is the only inmate. ==Issues involved==