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.

In Amazing Spider-Man #537, Peter Parker/Spider-Man meets with Captain America to offer his services to the anti-registration movement. After he and Captain America share a meaningful conversation, they head to the secret Avengers headquarters to meet other supporters and plan their attack on the Negative Zone prison. Meanwhile, at Ryker's Island Penitentiary, Wilson Fisk, the Kingpin of crime – albeit incarcerated – plans an attack on Peter Parker and his family. At issue’s end, the Kingpin's hired assassin, a sniper armed with a high-powered rifle – draws his cross hairs on Mary Jane and Aunt May from a building across the seedy motel room they share with Peter.

ACT 1: The sniper – the crosshairs of his high-powered rifle on Mary Jane Parker – is receiving further instructions from his superiors. He is to wait for the primary target – Peter Parker – to return and to hold off on the secondary targets until further advised. Inside the Parker seedy motel room, neither MJ nor Aunt May are aware that their lives are in danger. The phone suddenly rings. Aunt May answers. It is Peter and he wants to talk to MJ. As soon as MJ picks up the phone and hears his voice, she knows that something is going on. Peter tells MJ that things are about to get very bad and that he loves her very much. He then tells her that he will see her soon and hangs up.

ACT 2: Several hours later, the battle between the two sides of the Registration Act, which has been moved to the streets of New York City (see Civil War #7 to find out how that happened), is intensifying beyond belief. As Captain America and Iron Man battle it out, Spider-Man wonders if the citizens understand that they are not fighting for themselves or for the right to wear a mask, they are fighting for said citizens. He also hopes that these same citizens understand that the heroes, notwithstanding their sides, are fighting for their ability to be there, without any hesitation or condition, when the darkness comes and crime shows its head. Back at the seedy motel, Aunt May and Mary Jane are glued to the TV – watching as the events unfold.

ACT 3: In prison, inmates are watching the battle on TV while on a nearby set of stairs, the Kingpin speaks to one of his subordinates via a miniscule communication device implanted in his ear. The subordinate comments to the Kingpin that they might not have to pull the trigger after all, especially with the way the fight is going. The Kingpin replies that, if Spider-Man survives, they will take care of him when he gets home. If he is killed in action, then he wants Mary Jane and Aunt May taken out on principle because, after all, they will be so devastated by his death that killing them will be an act of mercy. Just then, an inmate calls to the Kingpin and tells him to check out what is happening on the TV (see Civil War #7 for further details of what is happening on that television screen). He then tells the Kingpin that he probably did not anticipate what just happened. The Kingpin replies that in every two-sided war there must – in the end – be one winner and one loser. He then says that the result of this war will serve them very well and smiles.

ACT 4: While the sniper waits for Peter Parker to return to the seedy motel room he shares with his wife and aunt, J. Jonah Jameson, at the Daily Bugle, has to choose a headline for the paper, based on the outcome of the war (what he chooses is not revealed here but for further details, see Civil War #7). The war now over, citizens walk through the rubble to survey the damage while heroes that stood at the end of the war rummage through the debris to help those that fell during the fierce battle.

ACT 5: Back at the seedy motel, Aunt May and Mary Jane watch the news where it is revealed that three heroes have not been located, one of which is Spider-Man. Hearing this news, MJ steps out of the room, triggering the small device the sniper put on the door in Amazing Spider-Man #537, thus warning him that the door has been opened. The sniper grabs his rifle and draws his crosshairs on MJ. Unaware that she has a target on her head, MJ walks around the parking lot, praying God that Peter will come home safe and sound and that she is willing to give up anything to see him again.

ACT 6: Cut to a quick scene explaining that the President is going to address the nation later that night to get the parties on all sides to come together in the best interest of the country and so as to put their differences behind them. It then cuts to the cemetery where Bill Foster, a.k.a. Goliath, is interred.

ACT 7: Across the seedy motel, the sniper waits for Peter Parker to return home. However, the wait proves too long for him and he falls asleep at his post. A short time later, Peter returns home. Opening the door to the room, he unknowingly activates the small warning device, which alerts the sniper of his return. The sniper takes his position at the window. As Peter tells Mary Jane that he is okay and unharmed, his spider-sense kicks in warning him of danger, though he does not know what is causing it to buzz like that. Just then, a shot rings out through the night, piercing the window. Peter tackles Mary Jane to the ground but as he looks up to check up on Aunt May, he is horrified to see that she has been shot in the abdomen.

To be continued.