After interrupting an arms sale between A.I.M. and Latveria is interrupted by Iron Man, who then takes the A.I.M. agents to the Vault. Bruce Banner is a prisoner in the Cube. Thor is visited by Balder who warns himabout the upcoming Odinsleep, but Thor tells he is more needed in Midgard and saves Jane Foster of an out-of-control cab. In the Big House, the miniaturized prison inside the S.H.I.E.L.D. Helicarrier, Henry Pym is interrogating the Mad Thinker about what he told Whirlwind about being free soon, while in other part of the Helicarrier, Wasp talks with Maria Hill about the possibility of becoming an agent.
Suddenly, all three prisons experiment a symultaneous failure; the Big House recovers a nrmal size, damaging the Helicarrier, and the failures in the Cube cause Samson to get exposed to Gamma radiation, becoming super-strong and green-haired.
Wasp and Ant-Man separately face some of the Big House escapees until they find each other. At the Cube, Samson saves Banner from debris, but is attacked by Zzzax, which causes Banner to get angry and turn into Hulk, who fights his way out, and the Leader lets him go to take over the Cube. At the Vault, Iron Man fights all the prisoners, even Hawkeye, despite him trying to stop the others.
Graviton is stopped from killing Fury by the intervention of Thor, Ant-Man and Wasp. Meanwhile, Iron Man goes to change armors as his was heavily damaged in the Vault. The Hulk leaves the injured Samson to be taken care of, and the Banner part of his mind tells him he could be seen as more than a monster if he helps people.
Even after Iron Man joins the battle, Graviton has the upper hand and lifts a chunk of Manhattan. Then Hulk arrives and turns the tide of the battle. By using their abilities together, the heroes defeat Graviton. S.H.I.E.L.D. agents try to recapture Hulk, but the other heroes defend him as he helped them to save the city. Nick Fury orders his men to stand down and invites the heroes to join S.H.I.E.L.D. to which they refuse but decide to form an independent team, which Wasp names Avengers.
Agent Quartermaine reports to Fury that Graviton didn't wake up until the malfunctions of the Raft had already happened, which leaves Fury wondering: if Graviton didn't cause the breakout, who did?