An eighteen-wheeler loses his load on the Brooklyn Bridge, leading to a traffic jam. The people on the bridge are doing normal things, trying to cope, when, suddenly, the bridge explodes.
Normal people and Ultimates alike are listening to the ensuing broadcast by the arch-villain Magneto, who, until this point, was believed to be dead. Magneto announces his return and that he intends to speed up his agenda. The Brotherhood of Mutants will take their place at the top of the food chain. As he dislikes speaking to humans, he will keep this message short: humanity has six months to surrender the world to Homo Superior. During that time, mutants will prepare the new society and decide which races "should be kept as slaves, which should be fuel, and which should be saved for the larder."
In the White House, President Bush and Vice-President Cheney demand an explanation from General Nicholas Fury. Why was Magneto believed to be dead? Because, Fury replies, according to Professor Xavier - not to mention five thousand eyewitnesses - Magneto was executed six months ago. The same Xavier who used to be an associate of Magneto's and who can control minds Cheney sardonically asks? Fury agrees, but also points out that Xavier and the X-Men saved the life of the President, his daughter and everybody else "in this room". Besides, this time they are not only relying on the X-Men, but also on the Ultimates - that's the kind of threat the team was created for. Cheney hopes that the Ultimates are effective, because, otherwise, they might have to look for a new Chief of Security.
At the Triskelion (the New York Headquarters of the Ultimates), the Wasp and Dr. Brankin are watching the rescue work at the Brooklyn Bridge on the screens. According to the Wasp, Iron Man and Thor are trying to help, but it's been ninety minutes since the explosion. They can't do much more than fish corpses out of the water. Captain America, Black Widow and Hawkeye are following some leads on the perpetrators the FBI gave them. Both Brankin and Janet are clearly shocked; they thought the Brotherhood had been neutralized and Magneto was dead.
In a hotel room in New Jersey, the six Brotherhood members who were responsible for the attack - Hard-Drive, Juggernaut, Mastermind, Rogue, Toad and Vanisher - are watching the news reports on their handiwork. Juggernaut comments that they could have caused more than eight hundred deaths if they had toppled the truck further up the bridge. The news reporter mentions that members of the Brotherhood are believed to be responsible for that attack and that the Ultimates are following positive leads to their whereabouts. Rogue gets nervous when she hears that, but Toad and Vanisher calm her. News reporters always say stuff like that to make the people feel better. It means nothing.
At that very moment, a gas grenade is thrown into the hotel room. Before they can react, Captain America jumps in through the window and easily keeps them off their toes with a skilful throw of his shield. Vanisher teleports out, where he is already expected by the Black Widow, who quickly takes him out with one kick. Toad jumps out of the window with the somewhat ungrateful Rogue, assuring her that he won't let Cap get her. Unfortunately, he lands badly, injuring his ankle, because of the extra weight. Even more unfortunately, they are already expected by Hawkeye - bow all ready - and several SHIELD agents.
Rogue assures them they won't make any trouble as long as her friend gets medical attention. Over the radio Cap tells Hawkeye not to trust her, but it's too late - Rogue has already touched Toad, absorbed his powers and now attacks the agents. She jumps away, over the cars, and one SHIELD agent radios the others that they've lost her. Hawkeye tells her to calm down and shoots a trick-arrow at Rogue, tangling her legs with the electrically charged trapwire that comes out of it.
At the Triskelion, Quicksilver and Scarlet Witch - the former, now disgraced Brotherhood leaders - are being escorted in by heavily armed agents. What are they doing here, Quicksilver complains. Their father is the most wanted terrorist leader on the planet and they are blithely walking into a U.S. army facility? That invitation has to be a trap. Wanda replies that they are hardly going to use them as bait, considering the Brotherhood now wants them dead. Besides, hanging with those supersoldiers is probably going to save them from their father.
Entering the conference room, Quicksilver haughtily asks the Ultimates not to stop gossiping about them on their account. Actually, they were discussing the new anti-terrorist measures he and Secretary Rumsfeld drew up this morning, Cap replies, but he's sure Wanda and Pietro could make valuable contributions. Black Widow interjects: she thinks it a foolish idea to have the two former Brotherhood leaders in the room, while they are plotting against their father. After all, they know what is said about leopards changing their spots? Cap replies that Wanda and Pietro proved themselves on a number of covert missions for the U.S Government, while at the same time toning down the Brotherhood activities and, if they are going to exclude colleagues with a colourful past, does that also apply to former KGB superspies? Touché Natasha admits.
Returning to the business at hand, Cap states that the main objective is to take down or kill Magneto, but the first priority is public safety. Therefore, at least one superhuman is going to be placed in every major city and mutants with known anti-human tendencies are to be detained. Thor protests that these measures had better be more humane than the Sentinel program. He is not going to tolerate another mutant witchhunt. The Wasp interjects that she is the last person to want an anti-mutant witchhunt, but the president has assured them that they are only detaining mutants with Brotherhood links and that they are doing so in accordance with the Geneva Convention.
Hawkeye wants to know where the X-Men are in all of this? Cap explains that Fury couldn't reach them on the hotline so he sent Iron Man to their headquarters to investigate. He then radios Iron Man who's standing in font of the X-Mansion with his SHIELD team. Stark admires the camouflage technology that hides Xavier's Mansion in plain sight. Viewed at a normal frequency, what you see is the local chapter of the Jehova's Witnesses. Switch to a secret frequency, however, and you see a beautiful Georgian mansion with Xavier's name on the front gate.
Since the perimeter scan isn't picking anybody up, they enter. Stark get the impression that Xavier's people left in a rush. Perhaps Magneto attacked them? Cap tries to stay optimistic, but then has a call from Fury, who tells him they just received intel on the X-Men situation and asks to be patched through to Iron Man as well. Iron Man reacts shocked, when he hears what Fury has to say. He then tells his SHIELD team grimly that he has just received the worst of news: Apparently, Xavier and Magneto managed to patch up their ideological differences. The X-Men have joined forces with the Brotherhood.