A Superhuman Registration Act is passed which requires all people possessing paranormal abilities to register with the government. Those who do not register are considered criminals. Some heroes, such as Iron Man, see this as a natural evolution of the role of super humans in society, and a reasonable request. Others view the Act as an assault on their civil liberties. After being called upon to hunt down fellow heroes in defiance of the Registration Act, Captain America goes underground and forms a resistance movement.

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.

In Amazing Spider-Man #533, Spider-Man takes off his mask and reveals his secret identity for the whole world to see.

In a brutal battle between the pro and anti sides of the Superhuman Registration Act, Bill Foster - the anti-registration hero known as Goliath - is killed. Other members of Captain America's resistance are captured and brought to the pro-registration faction's holding facility in the Negative Zone. Both sides retreat in order to regroup and plan their next move.

Many heroes are left injured, discouraged and questioning where they stand. While some of Captain America's allies are joining with Tony Stark, Spider-Man is beginning to question his loyalty to Iron Man – and the Invisible Woman and the Human Torch leave the pro-registration side and go in search of Cap’s underground, officially breaking up the Fantastic Four.

In Amazing Spider-Man #535, Peter Parker finally decides to make his move to the anti-registration side of the Superhuman Registration Act. After helping Aunt May and Mary Jane escape from Avengers Tower, Peter, as Spider-Man prepares to leave, only to be confronted by Iron Man.

In Amazing Spider-Man #536, Peter Parker/Spider-Man briefly battles Iron Man before escaping into the sewers. Peter later meets with Mary Jane and Aunt May, who are hiding in an abandoned school, and the three of them check into a seedy motel, where they hope they will not be tracked. Later that night, Peter, as Spider-Man, interrupts a news broadcast and reveals that he has switched sides and plans to join the anti-registration resistance movement. Needless to say, Iron Man is not very happy about this new development.

ACT 1: Peter Parker awakens bright and early, throws a ball cap and a pair of sunglasses on, and heads outside the motel to pick up the day’s newspaper. The Daily Bugle front page is obviously plastered with his picture and the news of his switching sides and desire to join the anti-registration group led by Captain America. Picking up a copy of the paper, he heads back towards the room he shares with Mary Jane and Aunt May. On his way there, he runs into a prostitute that lingers around the motel. They exchange a few words before he disappears into his room. What Peter does not come to realize is that the prostitute has just figured out who he is and intends to cash in on the reward for the capture of Spider-Man. She calls up one of her friends to let her know what she just discovered. What will happen remains to be seen.

ACT 2: At the secret Avengers Headquarters, Captain America sends the Human Torch (a.k.a. Johnny Storm) out on patrol to try and locate Peter and his family before Tony Stark does. A short time later, as Johnny circles the city, he tries to think of the best way to find Peter.

ACT 3: At the seedy motel, Aunt May asks Peter what the agenda is for the day. Peter replies that they are to lay low until nightfall and try not to attract any unwanted attention. Looking out the window, Mary Jane tells Peter that it may not be an option. When Peter asks why she is saying that, she tells him to come have a look out the window. As he does so, he sees a giant fiery spider up in the sky with the words "Call Me" underneath it – courtesy of the Human Torch.

ACT 4: At Ryker's Island Penitentiary, Wilson Fisk, the man who used to be commonly known as the Kingpin in New York City's underworld, is paid a visit by one of his subordinates. The man in question tells Fisk that they have located the individual of whom they have spoken previously and asks if, as an honest businessman, he wants this person to receive the bonus he is long overdue. Drawing the symbol of a spider on a sheet of paper and "+2", the man slides the paper across the table towards Fisk and says that he wants confirmation about whether or not the individual he is referring to is to get what is coming to him (spoiler: the individual is Peter Parker – Spider-Man obviously). After pondering the question for a few seconds, Fisk tells his subordinate that he wants the individual to get nothing but the very best, as soon as possible, in case he decides to move. Fisk then draws a target across the "+2" and tells his subordinate that he wants this to be the kind of surprise that just cannot miss. His subordinate asks what they are to do if the target moves before the package can be delivered. Fisk replies that they ought to deliver the package to anyone at home who can accept it because in the end, as with all gifts, it is the thought that counts.

ACT 5: In another part of the city, Captain America and the Falcon are discussing Spider-Man's recent decision to abandon Tony Stark and his pro-registration group. Falcon is hesitant to let Captain America try and find Peter because he fears it could be a trap. Captain America understands his concern but goes after Peter nonetheless.

ACT 6: A short time later, Spider-Man and Captain America meet on a rooftop. How they found each other is not explained. After a brief staring contest, Spider-Man speaks first and a lengthy discussion follows, where Captain America quotes Mark Twain to explain his decision to lead the anti-registration team. Spider-Man is utterly impressed and does not regret switching sides and joining the anti-registration heroes.

ACT 7: Several blocks away, Fisk's subordinate – last seen meeting with the big boss himself – is delivering the target information to a hired assassin (inside a parked car). He tells the assassin that he will only have, at best, one shot at the primary target, and what he decides to do with the secondary targets is up to him. He also tells the assassin that the target has a tendency to sense danger when it is coming so it may complicate the job. As the assassin steps out of the vehicle, he tells Fisk's subordinate that he has had to deal with this sort of thing before and has a little solution to that problem. It is called sleeping on the job, which is one of his two trade secrets. When asked what the other trade secret is, the assassin takes out a gun and shoots Fisk's subordinate in the head three times, concurrently telling him that it is to never leave a direct connection to a job alive to testify against you. The assassin then sets the car on fire and walks away nonchalantly. Minutes later, he knocks on the Parker's motel door and when Mary Jane answers, he asks if she needs fresh towel (he does this so he can find out if someone is home). She declines and closes the door, but not before the assassin can place some kind of device between the doorframe and the door. The assassin then drops the towels, walks across the street and relocates to the second floor of an abandoned building where he pulls out his rifle and draws his crosshairs on Mary Jane, who is looking out the window.

ACT 8: Somewhere in the sewers, Spider-Man, Captain America, and the some of the other anti-registration heroes, are making their way to the secret Avengers headquarters. On their way there, Captain America explains that there are three very important elements when planning out an engagement. You have to be sure you know what you know, you have to know what you don't know and there are always things that you don't know you don't know and those are the things that can get you killed. Captain America explains that they know Iron Man's resources, numbers and now – thanks to Spidey – his strategy. Yet, knowing so much makes him all the more concerned about trying to figure out what it is they do not know. Spider-Man tells Captain America not to worry too much, because he is the best tactical brain on the planet, which makes him believe that there is nothing he left out of the equation. As the issue ends, the assassin's crosshairs are still drawn on Mary Jane.

To be continued.