As conflicts rage and tensions rise, heroes on both sides change their allegiances, switching between the pro and anti-registration camps. Finally, the resistance mounts an attack on the pro-registration faction's holding facility in the Negative Zone. But Iron Man and his forces are lying in ambush.

The battle is joined...

ACT 1: Captain America yells his classic "Avengers Assemble" line and the battle begins. Bishop (of the X-Men) comments that he thought the pro-registration side was the Avengers, only to be taken down by Captain America himself. While the battle rages on, two S.H.I.E.L.D. agents are trying to close down the gateway back to Ryker's Island so that the heroes stay trapped inside the Negative Zone prison. Unfortunately for the two agents, Dagger and the Black Panther show up to stop them from doing so. The Black Panther sits down at the computer and starts rerouting the bridge to the Baxter Building. Aboard the S.H.I.E.L.D. helicarrier, Commander Hill is made aware of the Black Panther's attempt to reroute the gateway and tells one of her agents to close it down before they escape, or else he is out of a job. The Black Panther realizes that S.H.I.E.L.D. is onto them and that they only have ten seconds before the Baxter Building's portal is closed. Dagger immediately contacts Cloak and tells him that he needs to perform the biggest teleportation he has ever pulled. Cloak replies that he cannot, as there are too many people but Dagger convinces him to at least try or else they will be stuck in the Negative Zone forever. Extending his cloak as far as he has ever done in his entire life, Cloak wraps it around everyone.

ACT 2: Cloak dumps everyone outside the Baxter Building, in New York City. Those that can fly grab others that cannot; however, many crash to the ground, sending bystanders running for their lives. Enraged, Wonderman takes Cloak out for screwing up the plan. Nearby, Iron Man sends a message to all his men, telling them to evacuate the area and contain the fight to Midtown. The Human Torch tries to take Iron Man down from behind but the tin man has seen him coming and disposes of him rather easily. While police are trying to calmly evacuate the area, heroes are at each other's throat both on the ground and in the air. No matter where they are, all the heroes are fighting.

ACT 3: Spider-Man makes his way through a barrage of pro-registration heroes and lands a kick dead in the center of Mr. Fantastic's (a.k.a. Reed Richards) chest, sending him crashing to the ground. Close by, Iron Man asks that Captain America be located, as he is too dangerous to be left out there unchecked. On cue, Lady Deathstrike, Venom, Bullseye and the Taskmaster (a..k.a. the new Thunderbolts) attack Captain America. Despite his best effort, Cap is soon pinned in a losing position and taunted by Lady Deathstrike. But as Cap stares to the sky, a smile comes upon his face: his friend Namor arrives, the forces of Atlantis in tow, to help him. The anti-registration camp does not have much time to rejoice, however, because seconds later, the Thor clone shows up along with Captain Marvel and other super-powered supporters of the Registration Act.

ACT 4: Amidst the chaos, Captain America and Iron Man finally find each other. In the ensuing confrontation, Vision – on Cap's command – uses his phasing abilities to mess with Iron Man's armor, allowing Cap to deliver the first blow with his adamantium shield. The Thor clone witnesses this and tries to come to Iron Man's aid. However, Hercules intervenes and stops the Thor clone, telling him that he should fear for himself, not Iron Man. Nearby, a large bus is being pushed sideways to force some of the heroes to back away, prompting Sue Storm, the Invisible Woman, to check into it, only to discover that Ben Grimm, a.k.a. The Thing – back from Europe – is behind it. Ben alludes to the fact that he is on no one’s side and that he is simply there to help those that may unwillingly be caught in the battle, such as emergency personnel. A few feet away, the Taskmaster aims his gun at a distracted Invisible Woman and shoots. Having recuperated from his encounter with Spider-Man, Mr. Fantastic leaps in front of the gun blast and saves his wife. As Reed lies unconscious on the ground, Sue angrily turns her attention toward the Taskmaster and squashes him beneath an invisible force field. Not far from there, Hercules has gotten the upper hand on the Thor clone. Grabbing hold of the fake Thor's hammer, Hercules takes aim and delivers the deathblow, putting an end to the impostor's life.

ACT 5: With Iron Man's armor incapacitated, Captain America slams his shield repeatedly into his opponent's face, until his helmet's faceplate shatters. As Cap prepares to deliver the deathblow, he pauses momentarily as he contemplates what he is about to do. Just then, a group of normal citizens jump him all at once, telling him to get away from Iron Man. Cap begs them to let him go, as he does not want to hurt them, but they point out that it is already too late for that. An overview of where the battle is taking place shows the extent of the damage and destruction caused by said battle. Cap suddenly realizes that the men who attacked him are right. They are not fighting for the people anymore; they are just fighting amongst themselves. As he says that, he drops his shield to the ground. The Human Torch asks Cap what he is doing, commenting that they will be thrown in jail if they surrender. Spider-Man remarks that they were beating them, that they were winning the war. Tears streaming out of his eyes, Cap replies that they might have been winning the war, but not the argument. With that said, Cap takes off his mask and holds his hands out so the police can arrest him. As he gives himself up, he tells his men that they are not arresting Captain America, they are arresting Steve Rogers; he then tells them to stand down. Moments later, the Punisher picks up Cap’s discarded mask.

ACT 6: A montage shows (1) heroes joining forces to clean up the areas damaged during the battle; (2) Iron Man announcing the launch of the Initiative – at least one super-team in every U.S. state – and the formation of the new Mighty Avengers team, a new group of heroes based in Texas, and Canada's Omega Flight team; (3) super-villains that were used by Iron Man returned to the Negative Zone prison; (4) the secret Avengers – now led by Luke Cage – secretly meeting underground (with Spider-Man in his black costume); (5) Steve Rogers rotting in prison; (6) Hank Pym named man of the year by Time Magazine; (7) Tony Stark being offered the job of Director of S.H.I.E.L.D. by the President of the United States himself; and finally (8) Sue Storm returning to the Baxter Building to be with her family. Throughout the whole montage, a letter from Reed Richards to his wife Sue Storm is narrated and in it, Reed begs his wife to come back home. In the end, he gets his wish.

ACT 7: The S.H.I.E.L.D. Helicarrier, fives miles over New York City. Tony Stark meets with Miriam Sharpe, mother of a child who lost his life in the Stamford disaster, and announces to her that he has been named Director of S.H.I.E.L.D. She is surprised but Tony explains that, as a man with close links to both the government and the super human community, it makes perfect sense. Having said that, he asks Deputy Commander Maria Hill – who has obviously been demoted – to fetch them some coffees. They then take a walk where Tony explains that, though they won the war, they now have to win the peace. He wants people to get enthused about this new way of working they are hoping to initiate. He then tells Miriam that the State of Colorado has just requested the Thunderbolts as their official team, which he sees as a tremendous step to give offenders a second chance; something that they have tried to do as far back as the original Avengers. Tony then explains to Miriam that the reason they called the Negative Zone prison "Number 42" is because it was the number forty-two of a hundred ideas he, Reed Richards, and Hank Pym came up with the night her son was killed. Cleaning S.H.I.E.L.D. is number forty-three on the list. Tony goes on explaining that the superhero community just found the greatest friend they will ever have and that he would not let anyone else guard his friend's secret identities. Miriam tells Tony that he is good man and that, by risking everything to get them to this place, he has given people heroes they can believe in again. Tony answers that the best is yet to come.

The end.