In Amazing Spider-Man #529, Tony Stark, a.k.a. Iron Man, gives Peter Parker the new costume he designed for him. The costume has mesh webbing that can allow Peter to glide for short distances, heat resistant Kevlar micro-fibre that can resist small-calibre bullets, built-in fire, police and emergency scanner, audio and visual amplification, including infrared and ultra-violet, carbon filters in the mouth area to keep toxins out, and a short-range GPS microwave communication system, all routed through a computerized control system in the titanium chest piece. Finally, the costume is red and golden yellow. But with this costume comes somewhat of a price: Tony wants to hire Peter as his personal confident. After consulting with Mary Jane, Peter accepts the proposition and is then told by Tony to pack his bags because they are heading to Washington to face the Metahuman Investigations Committee of the United States Senate.

In Amazing Spider-Man #530, Peter Parker and Tony Stark head to Washington to try and talk the Senate out of forcing super-powered individuals to register their secret identity with the government or else face prosecution. While there, they come under attack by the Titanium Man. Peter dresses up as Spider-Man and takes him on. At issue's end, the Titanium Man takes flight with Spider-Man in tow.

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.

This issue picks up shortly after these events.

ACT 1: The story opens with Peter Parker asking Aunt May and Mary Jane to help him make a very important decision that will change his and their lives forever.

ACT 2: The next scene takes place a few days earlier. Peter and Tony Stark are coming back from Washington and discussing the events that occurred in Stamford, Connecticut. While they talk, Tony gets a phone call updating him on the above situation. After hanging up, he informs Peter about what he just learned, which is that the explosion took out a school filled with kids and that there are approximately 600 or more people dead.

ACT 3: Peter and Tony, as Spider-Man and Iron-Man respectively, head over to Stamford to help out. While there, Spidey notices that the people are staring at them in anger, obviously blaming them for what happened, though they were not involved. Iron Man comments that he does not and cannot blame them for hating them. When Spidey asks him what they are still doing there – having already helped digging out all the bodies – Iron Man points to a helicopter flying above them, inside of which is the President of the United States. He then proceeds to tell Spidey that he got a call from the White House asking him to be in Stamford so that he could see what the President was seeing, as he was seeing it.

ACT 4: A short time later, Tony meets with the President of the United States, while Peter waits outside. The meeting finally over, Tony comes out and updates Peter on what is going to take place. He first tells him that Congress will meet later that day to push through the Superhuman Registration Act, which – he thinks – will be signed within a week or so. He then tells him that the government wants superheroes to be identified, responsible, and controlled, starting immediately. Peter asks Tony if he is going to fight it, especially since he worked so hard to convince everyone he was not Iron Man anymore. Tony replies by making the startling revelation that he revealed to the President that he was in fact Iron Man. He then proceeds to tell Peter how he thinks the whole registration thing is going to pan out. Tony explains that, whether a good guy or a bad guy, the government will hunt down and arrest those who refuse to comply, along with anyone who aided or abetted them in keeping their identities secret. Consequently, their assets will be frozen, their homes seized, and finally, they will be jailed, some potentially for a very long time. Tony goes on explaining that this will split the powered community right down the middle and asks Peter if he will stand by him when it all comes crashing down. Peter replies that he will stand with him because he made a promise to him (back in Amazing Spider-Man #529). Tony goes on explaining that he will be taking the lead into making other powers register with the government and, as such, needs him at his side, both as Peter Parker and Spider-Man. Realizing that Tony wants him to reveal his secret identity, Peter tells Tony that he will do anything for him, but not that. Tony replies that if he does not unmask, then he will be breaking the law, and consequently, he will be hunted down like a criminal, as will Mary Jane and Aunt May, who will be considered accomplices. Finally, Tony adds that if he (i.e. Peter) turns against the law, then he (i.e. Tony) won't be able to protect him or his family. Having arrived at the airport, both Peter and Tony exit the limousine. Tony tells Peter that his plane will take him back to New York and that, if he does decide to stand by him, the pilot will bring him back. If he decides not to stand by him, then this is goodbye. Tony climbs back inside his limousine and heads back to Capitol Hill for another meeting with the President.

ACT 5: Onboard the plane taking him back to New York, Peter struggles with the decision he has to make. He calls his bank to figure out how much money he has saved, perhaps because he is thinking about running away.

ACT 6: Back in the present, Peter discusses the ramifications of going against the registration and Tony. With the aid of Mary Jane and Aunt May, Peter looks at the pros and cons of revealing his secret identity to the public. A heartfelt speech from Aunt May about how proud of him she is, no matter if he wears the mask or not, and amazing support from Mary Jane, convinces Peter to go along with revealing his identity to the world.

ACT 7: Four days later, Peter prepares to leave Avengers Mansion to head to Washington when Aunt May runs up to him and gives him one of his old costume, which she stitched up, so that the government officials know for sure that he is the real thing when they see him. She then offers a few last minute words of advice, as Peter stares at his costume.

ACT 8: The next morning, Peter meets Tony at the White House and tells him that he is keeping the promise he made to him by standing by his side. Tony appears delighted.

ACT 9: A few minutes later, Tony stands behind the podium in the White House press briefing room and introduces the leader of the pro-registration movement, Mrs. Miriam Sharpe, who lost her son in the Stamford incident. He then proceeds to introduce Spider-Man (we see Peter change into his costume and make his way to the press briefing room as Tony starts to introduce him). Spidey shows up in the room and takes the floor. As the issue concludes, he tells the media that he has an announcement to make.

To be continued.