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.

ACT 1: This issue opens with a recap of the battle that took place at the end of the recently released Civil War #3. Iron Man then congratulates his strike team, which includes Spider-Man, for being effective at capturing several members of Captain America’s anti-registration team. With that said, he gives them instructions to assist in the transport of the prisoners to a permanent holding facility across the city. As the heroes take their leave, Spidey stays behind, obviously upset about the recent battle. Iron Man has a brief conversation with him but it still does not change the fact that Spidey does not enjoy fighting his fellow comrades.

ACT 2: A short time later, a convoy of armored vehicle transporting the anti-registration prisoners passes through the city with Iron Man and Spider-Man at the head of it. As they move forward, Spidey can hear the crowd cheering for him; however, he can also hear them scream at him in anger, even going as far as calling him by his first name. Though he feels accepted for being on the side of the law, he cannot shake the feeling that he might have made the wrong choice siding with Tony. Spidey proceeds to ask Tony why he is riding shotgun rather than swinging up ahead. Tony explains that the other pro-registration heroes can react to trouble as it happens but he – Spidey – knows trouble is coming before it arrives, thanks to his spider-sense. Spidey is about to reply to Tony when he realizes that he's never told Tony about his spider-sense; the only two that know about it are Mary Jane and Aunt May. Spidey vows to check how much information comes into his suit and how much data goes out.

ACT 3: Spidey's spider-sense suddenly springs to life, warning him of danger. As a matter of fact, several feet below the ground surface, Captain America and his rather small anti-registration team, consisting of Luke Cage, Daredevil and Cloak and Dagger, are on the move. Back at the surface level, Iron Man instructs his team to switch to a pre-selected back up route, but as they prepared to do so, they find the route completely blocked by anti-registration protesters. Keeping his cool, Iron Man instructs his team to switch to another pre-determined alternate routing. When Spidey sees that they are heading for Yancy Street, he knows they're in for a heap of trouble because they are entering the Thing's neighborhood.

ACT 4: As they move along Yancy Street, they are bombarded with all kinds of objects thrown by its inhabitants, who are obviously against the Registration Act. While She-Hulk and the Wasp go on the defensive mode, Spidey focuses his spider-sense on a greater incoming danger: missiles. With some help from Mrs. Marvel and the Wasp, Iron Man destroys some of the missiles but two manage to make it through and are heading straight for Spidey. Spidey waits for the opportune moment and shoots two strains of webbing that snag the two missiles. He then changes their course by pulling on the webbing strains and he sends them crashing into each other, causing a massive explosion.

ACT 5: Looking down at the street below, Spidey notes the presence of the anti-registration strike team. Spidey drops down and comes face-to-face with Captain America. Cap cuts to the chase and tells Spidey that he respects him and that he would like to have him on his team, because he knows his heart and knows that he hates what he is doing and that he probably feels like there is no other choice. With that said, Cap extends his hand out to Spidey. Spidey hesitates, thinking about how he always wanted the respect of the people he admires, such as Captain America, and how it is being offered to him right there and then. In a dramatic turn of events, Spidey attacks Captain America. As they battle, Spidey soon realizes that Captain America’s fighting moves are well beyond his. They are powerful, smooth and quick, orchestrated like a ballet. After being on the receiving end of some very powerful punches, Spidey takes a few steps back to regroup and refocus. Restless, Captain America throws his shield, the symbol of the whole county, at Spidey. Spidey dodges the shield, as it bounces from wall to wall. Using his spider-sense, he determines where it is going to land and proceeds to web it against a nearby brick wall. But as he does so, he exposes his back to his adversary and the latter uses that opportunity to pummel Spidey in the ribs, making him numb below the waist. Spidey quickly regains his strength and starts thinking about how he is going to defeat his opponent. Realizing that Captain America knows his every move, his every skills and powers, which is why he wants to fight close, Spidey comes up with a plan and launches himself at him. As Spidey soars through the air, he deploys his extra appendages, which Captain America had not expected, and manages to draw first blood when one of his extra arms cuts Cap in the face. Cap is surprised and ticked and that's when Spidey realizes that the only way he is going to be able to defeat him is if he fights him man-to-spider instead of man-to-man. As he comes to that conclusion, a large explosion is seen and heard in the distance. Realizing that his fellow anti-registration team members are under attack, Cap heads to their rescue, leaving Spidey to wonder if he should take off after him. Spidey's thoughts are interrupted by a group of miscreants that are trying to steal Captain America's shield, which Spidey webbed to a wall during their battle. Spidey drops in and gives them a single warning to let go of the shield. The miscreants are easily convinced and take off like chickens with their heads cut off.

ACT 6: Spidey grabs hold of Captain America's shield and webs it in a place where nobody but Captain America can get to it, because he wants him to know that he left it there for him. Spidey hopes that once Cap finds it, he will understand that the shield represents the country, and the laws of the country decide who is right, even the laws nobody likes. Spidey surmises that Cap thinks in terms of right and wrong, but this isn't a matter of right or wrong, moral or immoral; it's legal versus illegal. At least, that's what Spidey tells himself when he wakes up at night, wondering what the heck he is doing. Spidey hopes to God that he is right.

To be continued.