In Amazing Spider-Man #531, Spider-Man defeats the Titanium Man, though the latter escapes. Facing the Metahuman Investigations Committee of the U.S. Senate, Tony Stark uses a video recording of the battle, taken from Spidey's new costume, to support his argument to not force superheroes to register their secret identity. Tony hopes that this will allow the whole process of the superhuman registration act to be delayed for a while. Peter Parker, who accompanied Tony in Washington, is suspicious that Tony may have had something to do with the Titanium Man's attack on Capitol Hill. Tony categorically denies his involvement so Peter abandons the notion. Later that night, Tony, as Iron Man, meets up with the Titanium Man and pays him for the earlier attack, thus revealing that he was actually the mastermind behind the attack. At issue's end, back in New York City, Peter watches a breaking news report on TV about a disaster in Stamford, Connecticut, that claimed the lives of at least six hundred people and countless more badly wounded. According to the authorities on the scene, the person responsible for all the devastation is a super-hero known as Speedball.

The story about what happened in Stamford Connecticut takes place in Civil War #1, the mega Marvel crossover for the year 2006. Speedball and fellow members of the New Warriors: Night Thrasher, Namorita and Microbe, are partaking in a TV reality-show in which they must battle super-villains. They arrive outside a house in Stamford, where four villains, Coldheart, Nitro, Speedfreek and Cobalt Man, are presumably hiding. The villains notice the young heroes and a battle naturally ensues. All but Nitro are taken down by the New Warriors. The latter tries to escape but Namorita corners him. Nitro retaliates by unleashing a devastating explosion that obliterates the small town of Stamford, and leaves but a few survivors. In response to this unforgettable event, the government decides to reopen the debate forcing super-powered beings to register their secret identity with the government or else face prosecution.

Superheroes gather together in Stamford to help find survivors and generally clean up. Iron Man informs Captain America that Nitro was spotted fleeing the scene in the back of a pick-up truck but Cap could care less for now, as he is too upset with the amount of lives that were lost for a reality show. The X-Men and a squad of Sentinels are there as well. Witnessing first-handedly such destruction and devastation leads the superhero known as Goliath to declare that this is the straw that broke the camel's back.

Tony Stark attends a memorial service for the Stamford victims and is blasted by an angry mother whose child perished in the explosion. The whole superhero community in general feels the backlash of the incident and many of them are blamed for the incident. Due to this, many superheroes, most notably Johnny Storm (a.k.a. the Human Torch), are attacked in public by angry civilians. To try and deal with the uprising of the population, heroes meet at the Baxter Building to discuss the Superhero Registration Act. Under the Act, the heroes would be given assignments by the government along with salaries and benefits. The major drawback of this is that heroes would also have to give up their secret identities. Obviously, the heroes are split on the issue.

Meanwhile, on the S.H.I.E.L.D. Helicarrier, Commander Maria Hill tries to entice Captain America to join them on a team that will force superheroes to register by tracking them down and arresting them. Taken aback by Hill's proposal, Cap refuses so Hill orders her men to take him down. Cap fiercely defends himself and makes his way out of the Helicarrier, supposedly going underground, perhaps to become the figurehead of the Anti-registration movement.

Back at the Baxter Building, Uatu, the Watcher arrives. Obviously, his arrival does not bode well because the Watcher usually only appears when events of universal proportions are about to take place.

At issue's end, Iron Man shows up at a meeting with the President of the United States and tells him and the other attendees to push ahead with the Superhero Registration Act and that, he, Mister Fantastic and Yellowjacket will take care of Captain America.

In Amazing Spider-Man #532, Peter Parker is given an ultimatum by Tony Stark: whether he joins him in his support of the Superhuman Registration Act, thus being forced to reveal his identity, or he is going to be hunted down like a criminal, as will Mary Jane and Aunt May, who will be considered accomplices. Peter spends the entire issue trying to make up his mind. After a lengthy conversation with his wife and aunt, Peter comes to a decision and flies off to Washington DC to partake in a press conference alongside Tony Stark. As Spider-Man, Peter joins Tony on stage and tells the media assembled that he has an announcement to make.

In Amazing Spider-Man #533, and on the last page of Civil War #2, Spider-Man takes off his mask and reveals his secret identity for the whole world to see. This comes as a surprise to many, including J. Jonah Jameson and Robbie Robertson of the Daily Bugle, as well as to some of Spider-Man's rogue gallery, such as Eddie Brock (a.k.a. Venom), Doctor Octopus, and the Vulture. However, there is still one person who refuses to believe this revelation: Flash Thompson.

Things go from bad to worse for the wall-crawling wonder. As he returns to New York, he is served with a lawsuit instigated by the Daily Bugle for misrepresentation, fraud, breach of contract, and several other related charges. Then, as he tries to spend some quality time with his family, he gets the unsettling news that he has been drafted, without consent, into Tony Stark's army of pro-registration heroes and, as such, he will have to fight fellow heroes that refuse to register with the government. When he confronts Tony about it, the latter apologizes and introduces him to the other strike team members: the Fantastic Four, minus the Human Torch, the Wasp, Doctor Samson, She-Hulk, Yellowjacket, Ms. Marvel, and the Thunderbolts, which consists of Baron Zemo, Songbird, M.A.C.H. IV, Fixer, Radioactive Man, Atlas, Joystick, Smuggler, Swordsman and Blizzard.

In Amazing Spider-Man #534, the story opens with a recap of the battle that took place in Civil War #3, between the pro-registration and anti-registration teams. After receiving congratulations from Iron Man for being effective at capturing several members of Captain America's anti-registration team, Spider-Man and fellow teammates are given the assignment of assisting in the transport of the prisoners to a permanent holding facility across the city. While escorting the convoy of armored vehicle transporting said prisoners, the pro-registration team comes under attack from Captain America and his team. In the ensuing battle, Spidey is offered the opportunity to switch sides from Captain America himself. But Spidey rejects his offer and continues to fight him. Their battle is short-lived but violent enough that Cap loses his shield to Spidey. When an explosion is heard in the distance, Cap stops the fight and heads to his friend's rescue, leaving Spidey to wonder if he should take off after him. His thoughts are interrupted by thugs trying to steal Captain America's shield, which he left behind. Spidey scares them away and proceeds to web the shield in a location where nobody but Captain America can get to it. At issue's end, Spidey starts to have doubts about his choosing the pro-registration side.

This is where this issue picks up.

ACT 1: It is late at night. Peter Parker is watching the news on TV. The anchors are discussing the recent award of billion-dollar no-bid contracts to Stark Enterprises and Fantastic Four Incorporated for the development of holding facilities and ancillary research and development. When Peter hears this, he concludes that this is the reason why Tony (Stark) and Reed Richards are so much in favor of the Super Human Registration Act.

ACT 2: Peter finds Tony in his study and confronts him about the contracts being awarded to him and Reed. Tony brushes off his comments and tells Peter that if he has something to say, he should not hold it back and should say what’s on his mind. Seeing as this is going nowhere, Peter changes the subject and asks that Tony take him to see the detention facility that he has been working on. Tony acquiesces to his request.

ACT 3: Tony and Peter head over to the Fantastic Four Headquarters where they meet with Reed Richards, a.k.a. Mister Fantastic. Reed activates all kind of weird devices and opens a portal into the Negative Zone, which is where the detention facility is located, to Peter's utter amazement. After putting on a thruster pack, as suggested by Reed, Peter enters the Negative Zone with Tony, as Iron Man. After a few minutes of flying, they arrive at their destination. As they enter the detention facility and make their way through a horde of security scans, Tony explains all the different safety measures that have been put in place to ensure that no one escapes. Tony reassures Peter that they do all they can to make the prisoners comfortable during their stay and even provide virtual reality systems for those who do not represent a tech-threat. Peter is not easily swayed, as every prisoner he sees is begging to be let out. Peter tells Tony that the prison seems like a good enough solution for the time being, which prompts Tony to snap at Peter and tell him that this solution is permanent, so he ought to "get with the program". Peter is confused and asks Tony if the prisoners are in there for life. Tony replies that they have the choice to either sign up, or they stay imprisoned until they do sign up; and if they never sign up, then they stay imprisoned for the rest of their natural lives. Peter tells Tony to take off his Iron Man helmet and repeat that again so he can see his face. Taking off his helmet, Tony tells Peter that he did not work his entire life to become someone's jailer. He hates this as much as he does and hasn't had a good night's sleep in weeks. However, he feels like he has no other choice than to follow the law. Peter replies that following the law means that they (meaning those that do not register) get a trial before they are sent away to be imprisoned for the rest of their lives. Peter feels that Tony cannot just lock them away. Tony retorts that they can, they have, and that they'll continue to do it. Peter argues that She-Hulk has been in court every day, making motions and defending those that refuse to register. Tony replies that her actions are fruitless, as the Super Human Registration Act is outside the jurisdiction of local and federal courts. Only the Supreme Court can intervene but Tony happens to know that they won't. Putting his helmet back on, Tony continues explaining that the Negative Zone is not on American soil; therefore American laws are not enforceable and American lawyers do not come here. Once non-registrants are in the Negative Zone, they are legal nonentities, occupants, and prisoners. This also applies to those who give them aid and support. Tony concludes by saying that he agrees with Peter regarding the fact that it would be a terrible thing to be stuck in the Negative Zone for the rest of one's life. The way Tony says it seems to imply that if Peter breaks the law, he will end up there as well.

ACT 4: A short time later, Peter and Tony return to the Fantastic Four Headquarters via the portal. While Tony heads to the bathroom, Peter stays behind and asks Reed why he is on the pro-registration side. Reed tells Peter the story of his Uncle Ted, an eccentric and colorful man, who did not care for rules and who was brought in front of the House Un-American Activities Committee where he was accused of being a Communist. His uncle could have denied the charges against him but he did not and he told them to go to hell. The government ended up holding him on contempt of congress for six months and when he got out, his career as a writer was over. Nobody wanted to hire him, buy his stories or even answer his phone calls. Even Reed's father refused to let him come around the house. In the end, it killed him (Uncle Ted). Peter tells Reed that his uncle was a very brave guy. Reed replies that his uncle was wrong and picked a fight he could not win. Whether HUAC was right or wrong was not the point. It was the law and his uncle broke the law. Reed supports the law because he honestly believes they have to, not matter what. Peter asks what he is supposed to do if he thinks the law is wrong. Reed replies that it will eventually be changed, in an orderly lawful way. With that said, Tony returns from the bathroom and he and Peter leave.

ACT 5: Outside on the balcony, Tony tells Peter that he needs him to go to Los Angeles for a while, on his behalf, as he is working on a new program called the fifty-state initiative and he needs his help out there. Peter asks why in L.A. and not in New York. Tony replies that he feels that it would be a good idea if Peter got away from New York for a while, so as to give him a break. Peter argues that he does not need a break and adds that he needs to stay for Mary Jane and Aunt May. Tony tells Peter not to worry about them, because as long as they are with him, they are safe. As Tony takes off flying, he tells Peter that he has things to do but he'll have the jet ready for Peter to leave first thing the following morning.

ACT 6: A short time later, Peter avoids the security cameras in Avengers Tower and proceeds to get MJ and Aunt May out of bed and into the kitchen where he disables the cameras. Peter tells them that they need to get out of there immediately, as it is not safe. He explains that he's made a terrible mistake – siding with the pro-registrants – and he is going to pay a price for both that mistake and any attempt to undo it. Suddenly, ominous "booms" are heard in the distance. Peter yells at them to leave now and switches to his Spider-Man costume. He heads down a hallway, bouncing from walls to walls when he is suddenly tackled by Iron Man, who comes crashing through a wall.

To be continued.