After Stamford, Connecticut is destroyed during a televised fight between the New Warriors and a group of dangerous villains, public sentiment turns against super heroes.

Johnny Storm, the Human Torch, is attacked outside a night club and beaten into a coma. Advocates call for reform, and a Superhuman Registration Act is debated, which would require all those possessing paranormal abilities to register with the government, divulge their true identities to the authorities and submit to training and sanctioning in the manner of federal agents.

One week later, the Act is passed. Any person with superhuman powers who refuses to register is now a criminal. Some heroes, such as Iron Man, see this 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 to hunt down heroes in defiance of the Registration Act, Captain America goes underground and begins to form a resistance movement.

The Amazing Spider-Man, who has allied himself with Iron Man and the pro-registration side, not only registers, but also unmasks as Peter Parker in front of the media.

Following a report of an explosion at the Geffen-Meyer Chemical Plant, Captain America and his resistance force arrive on the scene to aid in the rescue of the plant workers only find themselves in the middle of an Iron Man led – S.H.I.E.L.D. ambush.