In 1945 Japan, Steve Rogers staggers into a secret HYDRA Base hidden in the mountains. He is greeted by Kraken, a HYDRA commander and Rogers' former teacher. Kraken exposits that Rogers pretends to be on the Allies' side while secretly passing information to HYDRA. He takes Rogers to the center of the base and reveals that it stands on the ruins of a lost city called Ashomia. Kraken's own teacher, whom Kraken claims founded HYDRA using dark magics discovered in Ashomia, is present and reveals that—though HYDRA will win World War II absent outside interference—his divinations predict that the Allies will use a cosmic cube to rewrite reality so that they win the war instead. He tells Rogers that 'the usurper' (Elisa Sinclair) will eventually use 'the shaper womb' (Kobik, the sentient cosmic cube) to enable Rogers to remember the world as it should be, with HYDRA victorious. Rogers' job, says Kraken's mentor, will be to do everything in his power to bring HYDRA's victory about and restore the world to how it should be. He then senses that the Allies have begun to rewrite reality, and Kraken directs Rogers into a pool that will protect him from the effects of the Allies' cosmic cube. It gives Rogers memories of being a loyal Allied soldier, altering him before the Allies' cube does, and Kraken tells Rogers to never forget his true identity of a HYDRA champion.
In the present day, Rogers is now the Director of SHIELD. He and Sharon Carter command the defense of Earth while on a helicarrier. A gargantuan chitauri invasion fleet is attacking, and though Captain Marvel recently had a planetary shield built to protect Earth, a HYDRA suicide bomber damaged one of its generators and the shield is not working. With Rogers' assent, Captain Marvel leads a team of heroes including America Chavez, Spectrum, Blue Marvel, Quasar, Hyperion, Star-Lord, Gamora, Rocket, and Groot into orbit in a last-ditch attempt to hold off the invasion force while Riri Williams and the Tony Stark AI try to fix the generator and get the shield online. Quasar is particularly effective, being able to instantly kill anything she sees, but the invasion force stretches back for planets and even she cannot seriously dent the Chitauri. Simultaneously, a large army of supervillains attacks New York in revenge for SHIELD having altered their minds and trapped them in the Pleasant Hill 'prison' in an attempt to reform them. Luke Cage leads a large group of heroes, including Jessica Jones, Iron Fist, Daredevil, Spider-Woman, Wasp, Cloak, and Dagger to fight them off. Finally, HYDRA has conquered the nation of Sokovia and now controls its seven nuclear warheads. HYDRA leaders are threatening to use the warheads against European targets if their control of Sokovia is not formally recognized by SHIELD. SHIELD's helicarrier in the region stopped responding to hails and Carter fears it may have been hit with one of the nuclear warheads, so the bulk of SHIELD's helicarrier fleet is en route to Sokovia to deal with HYDRA.
In space, Hyperion is injured and Quasar is killed, badly reducing the strength of the hero team. The New York team also runs into trouble when a supervillain named Nuke detonates himself and Jessica Jones struggles to contain the blast. The American government declares a state of emergency and invokes a law allowing the Director of SHIELD to run the country and its military while the civilian leadership goes into hiding. Rogers accepts his new authority, then says "Avengers, Assemble" as a signal to various forces to implement the next stage of the plan.
The generator comes back online and the planetary shield reactivates. The chitauri drones cannot break through the shield and are too unintelligent to avoid crashing into it, allowing the space force to just stand back and let the invasion fleet destroy itself. Furthermore, Doctor Strange, Rogue, and the Uncanny X-Men arrive in New York to reinforce the heroes, and the villains quickly fall back. Finally, the missing helicarrier reestablishes communications. The heroes are jubilant at the turnaround, but then the missing helicarrier crashes into Rogers' and Carter's ship and Doctor Faustus hypnotizes the SHIELD defenders to let HYDRA board them. When HYDRA forces reach the bridge, Rogers admits he's the new leader of HYDRA and has a disbelieving Carter arrested.
Meanwhile, Williams and the Stark AI are confused as to how the shield was fixed. They conclude that the shield was never damaged; it was turned off by somebody, and the suicide bomber only did cosmetic damage to mask the real cause of the shield being off. Then Rogers contacts Marvel and tells her that the reason the chitauri are invading is that a Soviet scientist named Ivan Kragoff obtained a chitauri queen, and the chitauri will send unlimited waves of troops until they recover her. He tells her that he's turned on the shield to prevent any of the space heroes from getting back to Earth; the heroes are now trapped outside Earth and will eventually be worn down and killed by the endless chitauri force. In New York, a supervillain named Baron Zemo uses the Darkhold to trap the entire city in the Darkforce Dimension, cutting all of the heroes in the city off from the rest of the world.
With most of the world's strongest heroes trapped in space or the Darkforce Dimension, Williams and the Stark AI call for every remaining hero that can hear them to defend Washington D.C., which they anticipate HYDRA will attack next. Several heroes, including Jane Foster, Ben Grimm, Scarlet Witch, Vision, Spider Man, and the Champions, respond to the call. Helicarriers hijacked by HYDRA, however, are already hovering over the White House.
Tropes:
- Explain, Explain... Oh, Crap!: Twice with Riri and Tony. First, them going over the data on the shield generator and realizing it was already shut down and the bombing a cover for it. They then start talking about who to call in for reinforcements and realizes everyone is either up in space or in New York.
- The Mole: Captain America reveals himself as this.
