In response to this tragedy, public sentiment is turning against super heroes. Johnny Storm, the Human Torch, is attacked outside a nightclub and beaten into a coma. Advocate Miriam Sharpe, who lost her son in the Stamford Disaster, calls for reform in the way super heroes conduct their affairs. On Capitol Hill, a Superhuman Registration Act is debated which would require all those possessing paranormal abilities to register with the government, divulging their true identities to the authorities and submitting to training and sanctioning in the manner of federal agents.

Some heroes, such as Iron Man, see this as a natural evolution of super humans in society, and a reasonable request. Others, embodied by Captain America, take umbrage at this assault on their civil liberties.

When Captain America is called upon to hunt down his fellow heroes who are in defiance of the Registration Act, he chooses to go AWOL, becoming a public enemy in the process.

In a closed door meeting with the President and his Cabinet, Iron Man, Mister Fantastic and Yellowjacket vow to bring Cap to the ground.

ACT 1: The story opens with the discovery, by S.H.I.E.L.D. agents, of the Vulture and Grim Reaper, tied to a large pillar, supposedly having been put there by none other than Captain America, who, despite being against the Registration Act and thus a fugitive, continues to apprehend criminals. The lead S.H.I.E.L.D agent reports back to his commander, Maria Hill, whose worst fear becomes reality when she realizes that Captain America is not on his own anymore and that others have possibly joined him.

ACT 2: Meanwhile in New York City, a group of super heroes, comprised of Iron Man, Yellowjacket, Mrs. Marvel, She-Hulk, Reed Richards/Mister Fantastic, Tigra, and Doc Samson have taken down a Doom-Bot to the thunderous cheers and applause of bystanders. Iron Man comments that people are starting to believe into super heroes again, which prompts She-Hulk to ask him if there will be super heroes after the Registration Act is passed or if all of them will be S.H.I.E.L.D. agents on federal payroll. Iron Man replies that the purpose of the Act is to weed out kids, sociopaths and amateurs that called themselves heroes. Tigra jumps in the conversation and asks Iron Man in which category Captain America falls in. Iron Man simply replies that Cap is wrong and that she should trust him.

ACT 3: A short time later, at the Baxter Building, Home of the Fantastic Four, Reed Richards and his wife, Sue, are discussing the Registration Act and Reed’s involvement with a classified project, called "42", which is helmed by Tony Stark/Iron Man. Reed explains that he decided to side with Tony and the Registration Act because his calculations have shown that, if the unlicensed superhero activities are not brought under control, the results will be exponentially cataclysmic. When Sue asks him about the above project, he replies that he cannot tell her, as it is classified information. She does not appear to be pleased with his answer and mentions that she is off to see her brother, Johnny Storm, who lies comatose in the hospital. Absorbed in his work, Reed tells Sue to give Johnny all his love.

ACT 4: Meanwhile at the Daily Bugle, J. Jonah Jameson and Robbie Robertson are discussing the Registration Act. Jonah comments that everything the Bugle has ever campaigned for will officially become law later that night at twelve o'clock. Robbie asks him if he really thinks super heroes are all going to sign up. Jonah replies that the smart ones will, just as Spider-Man swings by his window.

ACT 5: That evening, at Tony Stark's penthouse, Tony sits with Happy Hogan and anxiously awaits the official legislation of the Registration Act. Tony asks Happy if he's heard from Captain America. Happy explains that Cap has been putting together his own team and will see this thing to the finish. Tony sure hopes he is doing the right thing.

ACT 6: Twenty four hours after the Registration Act becomes law, the super hero known as Patriot, a member of the Young Avengers, is on the run from a S.H.I.E.L.D. helicopter, because he tried to stop a robbery in costume and is unregistered with the government. The dispatcher tells the chopper pilot that he has permission to use tranquilizers and minimum force. The pilot complies and shoots a few rounds of tranquilizer darts at Patriot. Luckily, Patriot is bulletproof so the darts just ricochet off him. While the pilot digests this information and updates the dispatcher to get his new orders, Patriot leaps off one building and crashes into the offices of an adjacent one. As he gets back to his feet to contact the other Young Avengers, the chopper closes in on the building and unleashes a bomb that levels the whole floor where Patriot is hiding. Needless to say, Patriot is apprehended and taken into custody along with the other members of the Young Avengers: Hulkling, Wiccan, Hawkeye, Vision and Stature.

ACT 7: Elsewhere, Daredevil and Luke Cage are monitoring the capture of the Young Avengers. Daredevil asks Luke if they should get a posse together and intercept. Luke replies that Captain America and the Falcon are already undercover on the scene.

ACT 8: Thankfully for the Young Avengers, none other than Captain America in disguise is driving the vehicle transporting them to their holding cell. While Cap disposes of the real S.H.I.E.L.D. agent sitting next to him by kicking him out of the moving vehicle, which sends him flying into the path of the police escorts and causes a pile up, the Falcon, disguised as an agent in the back of the vehicle, proceeds to break Wiccan's shackles off and tells him to rustle up one of his teleportation spells to get them all out of there. Wiccan does as told and after a few minutes of nerve-racking tension, he teleports them all to some kind of huge headquarter where Daredevil, Cable, Luke Cage, Cloak, Dagger, Hercules and Black Goliath welcome them into the resistance team. As her shackles are taken off, Hawkeye asks where they are. Captain America replies that they are in a S.H.I.E.L.D. safe house only known to one person, Nick Fury, who is also underground and working on getting them new secret identities. Patriot asks why they need new secret identities and Cable explains that their old ones have been compromised. Cap then explains that it is where they are going to live and where they are going to start to fight back against Tony Stark and whatever he is planning out there. Just then, Dagger interrupts them and tells them to come watch a monitor displaying Tony Stark at a press conference in Washington D.C.

ACT 9: Tony Stark steps up to the microphone and introduces Miriam Sharpe, who lost her son in the Stamford incident and kick-started his passion for the federal employment of all super heroes. At the Xavier Institute in Manchester, the X-Men watch on, as Spider-Man, wearing his old costume, drops in on the stage and steps up to the mike. At the hospital, Sue Richards also watches the press conference and hopes that Tony knows what he is doing. Back at the press conference, Spidey starts by mentioning that he's guarded his secret identity pretty carefully over the years and that he's made a decision, after having a long conversation with his wife and family. He explains that super heroes have two choices: one, they can continue the trend that Captain America advocates and have people with powers completely unchecked or two, they can go legitimate and earn back a little public trust. At the Daily Bugle, Jameson tells Gloria Grant to not even think about asking him what he wants for breakfast or else she is fired. Needless to say, he is beyond excited and totally riveted to the TV screen. Back at the press conference, Spidey tells the crowd of reporters that he is not wearing his old mask because he is ashamed of what he does. In fact, he is proud of who he is and he is there to prove it. Having said that, Spidey takes off his mask and introduces himself as Peter Parker and tells them that he has been Spider-Man since he was fifteen years old. At the Bugle, J. Jonah Jameson passes out while hundreds of camera flashes and Peter asks the reporters if they have questions.

To be continued in Civil War #3.