Magneto's back and out for blood. The first thing his Brotherhood of Mutants does is blow up the Brooklyn Bridge, killing eight hundred in the process. Magneto then broadcasts a message telling Homo Sapiens they have six months to give the planet over to their rightful successor - Homo Superior. In Washington, the President and the Vice-President debrief General Fury on the debacle: why was Magneto believed to be dead? While one group of the Ultimates help with the relief work at the site of the attack, another team, led by Captain America, finds the responsible Brotherhood members, who believed themselves to be safe in New Jersey, and takes them in after a short fight. Later, the former Brotherhood leaders, Quicksilver and Scarlet Witch, join the Ultimates in their debate how to handle the fight against Magneto. In the meantime, Iron Man examines the empty X-Mansion, trying to find out where the X-Men are, as they could use their help. At that moment, he receives a message from Fury. Apparently, Xavier and the X-men have joined Magneto's cause.
Wasp tries in vain to get some information on the X-Men's current whereabouts from Marvel Girl's father. In the meantime, the X-Men have hidden in a New York safe house and Xavier compares notes with Moira MacTaggert, who had to evacuate to Glasgow. Beast is trying to build a secure line to the Ultimates and becomes angry when Storm forgets to bring some material he needed from her shopping expedition. Angrily, she snaps that this whole mess I his fault anyway. They are interrupted as the X-jet with the missing members, returns from the Savage Land, but Cyclops is not with them. According to Wolverine, he's dead. In the meantime, the Ultimates are planning their strategy when the building is attacked by Magneto. He easily brushes aside both soldiers and Ultimates, punishes his children by shooting Quicksilver into hiskneecaps and then informs the Ultimates that he has erased all information on the Brotherhood from their computers. With that he leaves. Shortly afterwards, SHIELD agents inform Captain America that Xavier has contacted them and wants to broker a deal. Cap brusquely refuses: the X-Men are going to be brought down as hard as Magneto and the Brotherhood.
President Bush is evacuated to L.I.N.C.O.L.N., a secret base that looks like an innocent small town. At the Triskelion, the Ultimates learn that the Hulk managed to escape during Magneto's attack and Captain America tells the Wasp that they all know about her being a mutant and that it doesn't matter. Elsewhere, while Jean is harbouring suspicions that Wolverine might have had a hand in Cyclops' death, Xavier arranges a meeting with Magneto's agents - seemingly to arrange for a compromise between their two groups but actually to track the agents back to their homebase. Two can, however, play at that game. Magneto does the same and then anonymously tips SHIELD off... and the Ultimates attack...
It’s an all-out battle between the Ultimates (supported by SHIELD troops) and the X-Men. Despite being more battle-savvy than most of the Ultimates, the X-Men are being taken out one by one. Even Wolverine is beaten by Captain America and Colossus falls to nothing less than a small-sized nuclear warhead. The cavalry arrives in the form of Iceman who freezes all of SHIELD’s technology, including their neural scramblers, allowing Xavier to access his telepathy once more and freeze every non-mutant brain on the block. However, one of the Ultimates – the Wasp – is a mutant as well and she uses her tactical advantage to take Xavier out with her wasp stings, not before he orders the X-Men to escape though, which they do. Later, with Xavier in prison, Magneto lets him know that he instigated all of this to get his hands on Xavier’s students, who will, without any doubt, sooner or later turn to him.
First Story: Professor X goes about recruiting new mutants for his team of X-Men. There are seven in all and each one of them agrees, although some reluctantly. The mutants are Nightcrawler, Wolverine, Banshee, Storm, Sunfire, Colossus and Thunderbird. They all gather at Xavier’s school where they discover their purpose, to rescue the original X-Men. Cyclops, the only survivor from the first crew, fills everyone else in on what happened, how the X-Men went to the island of Krakoa and disappeared. The new X-Men saddle up and hitch a ride on the Strato-Jet with Cyclops to the mysterious island. They break off into pairs upon arrival in order to cover more ground quicker. Each team runs into trouble on their way to a mysterious temple that appears in the middle of the island. Once they all arrive at the temple they break in and find all of the X-Men strung up by tubes and being fed upon. They break them free as the temple starts coming down. Safely outside, the original X-Men come to. Angel begins filling them in on what happened when the island itself opens up before them. A humanoid being emerges and explains that it itself is the mutant they were looking for. The entire island of Krakoa is a mutant. Krakoa explains that it was feeding off of the X-Men and let Cyke go free to bring back more mutants. Immediately following the explanation, battle commences. Nothing the X-Men throw at it is effective. Professor X contacts Scott after watching the battle for a bit and tells Scott his master plan. The plan involves Lorna Dane severing the planet’s primary lines of magnetic force. It works and Krakoa is expelled into outer space. Iceman creates an encased ice raft to save them out on the ocean. When all is calm all thirteen X-Men board the floating Strato-Jet and head for Westchester.