During a televised raid of a house containing select villains that had recently escaped from the super villain facility at Ryker's Island prison during a massive breakout, the escaped villain Nitro let off a massive explosion that killed the majority of the New Warriors, as well as the children at a nearby elementary school. In the wake of the tragedy, the U.S. Government proposed the Superhuman Registration Act, intending to register all super-powered beings as living weapons of mass destruction and requiring all costumed heroes to unmask themselves before the government and subject themselves to federally mandated standards.
This event triggered negative public opinion against the super-heroes, resulting in the assault of Human Torch (Johnny Storm) by a mob and the request by S.H.I.E.L.D. for Captain America to become part of the enforcement of super heroes to register. When Cap refused, S.H.I.E.L.D. Director Maria Hill ordered S.H.I.E.L.D.'s Anti-Superhuman Response Unit to tranquilize him, but Rogers escaped and went underground.
When the super-heroes met to discuss the best course of action, Uatu the Watcher appeared. As Watchers only appear to monitor key events throughout history, it was noted that his presence did not bode well for the heroes.
In a secret meeting with the President, Iron Man suggested that the President proceed and push the registration act while he, Mr. Fantastic, and Yellowjacket vowed to bring Captain America to the ground.
The Superhero Registration Act became law. Some of the first unregistered heroes to be captured were the Young Avengers. Captain America and the Falcon were undercover, and with the help of Wiccan were able to rescue the Young Avengers and rendezvous to their base. The Young Avengers were recruited into the Resistance.
At a press conference in Washington D.C., Iron Man gave a speech introducing Spider-Man to the podium. Spider-Man then talked about how over the past years, he had kept his identity a secret, then talked about the registration act and how it gave superheroes a choice: to continue the trend Captain America advocated and have people with powers completely unchecked, or that superheroes could go legitimate and earn back a little public interest. To demonstrate his support of the Act, Spider-Man unmasked himself and revealed to the world that he was Peter Parker.
Iron Man traveled to the X-Men Mansion, asking Emma Frost if the X-Men would sign the registration act and join his side. Miss Frost explained to Stark that the X-Men would not sign the registration act because they viewed hunting down other heroes would violate everything they stood for explaining that they know what it's like to fight the good fight while being persecuted. Frost said that as long as the pro-registration side left the X-Men alone, they would not join Captain America's resistance. While Stark left the mansion, he was approached by Bishop, who asked for a word with Iron Man.
As Captain America, Hercules, Daredevil, and Goliath were discussing their new secret identities, they received news of a petrochemical plant fire with three or four hundred workers trapped inside. Uniting the Secret Avengers, they headed to the plant only to discover that it was a trap set by Iron Man. Iron Man gave Captain America one last chance to register, offering a chance to explain things. Captain America answered by striking the first blow and disabling Iron Man's armor. A battle ensued, ending with Iron Man savagely beating Captain America, and the apparent return of the long-absent thunder god Thor lashing out against Captain America's Secret Avengers. As the Secret Avengers attempted to escape, Thor used his hammer to subdue them, blasting a hole through Goliath’s chest when he was attacked. Thor continued his assault until the Invisible Woman used her powers to protect the Secret Avengers and allow them to escape. Thor, who had just killed Goliath, was revealed to be a clone. He, and his mechanical hammer, had been engineered to serve the government. His violent murder of Goliath was an unforeseen error in his programming.
The death of Goliath opened the eyes of many and put things in a different perspective, causing several members to leave both sides for the other. The Pro-Registration side ended up losing more members than anticipated, causing operations to be put in action faster than planned. Iron Man assembled a new group of Thunderbolts in order to hunt down the Secret Avengers, consisting of several very brutal villains.
Eventually, the resistance mounted an attack against the pro-registration's holding facility in the Negative Zone, releasing the prisoners. The fighting between many of Earth's heroes led to the middle of Times Square. At the climax of the battle, as Cap was about to deliver a finishing blow to Iron Man, he was tackled by several emergency workers. Realizing the damage the war was doing to the city and its civilian population, Captain America unmasked and surrendered. Before his arraignment, Cap was shot multiple times on the steps of a Federal Courthouse and killed.