Previously, the X-Men defeated Magneto and pronounced him dead. Rather than turning Magneto over to the authorities and virtually ensuring the death penalty for him, Professor X secretly brainwashed his old friend and tried to rehabilitate him. However, the Beast inadvertently leaked this plan to Magneto's Brotherhood, believing that he was chatting with an online girlfriend. The Brotherhood use this to entrap Beast and gain enough knowledge to free their leader.
The X-Men were in a difficult enough situation as it is. Iceman had left the X-Men forced out by his worried parents after he sustains injuries in the fight against Proteus. Three X-Men, Wolverine, Cyclops and Kitty Pryde, were on a mission to the Savage Land.
The US government is irate over Magneto's reappearance and demanded explanations from Nick Fury. Fury and his Ultimates tracked down the Xavier Mansion, whose location was hitherto unknown, and found it empty. Nick Fury comes to the incorrect conclusion that the X-Men have joined forces with Magneto to fight mankind.
In preparing to battle the X-Men, Captain America reveals he knows more about Wolverine; they fought together in World War 2, when Logan went under the name James "Lucky Jim" Howlett. The X-Men's plane returns, with only Logan and Kitty on board. Wolverine claims Cyclops had died heroically. The truth, which Jean later learns, is that Wolverine had tried to kill Cyclops so as to be with Jean.
In the meanwhile, Charles Xavier meets with Magneto to negotiate a truce. The meeting was actually meant as a diversion in order to give Wolverine time to track down Magneto's location. Unbeknownst to the Professor, Magneto had anticipated Xavier's double-cross. While Wolverine tries to locate the Brotherhood, Magneto anonymously tips off the X-Men's whereabouts to the Ultimates. The Ultimates track down the X-Men and have an all-out fight.
The Ultimates nearly defeat the X-Men, but at the last moment Iceman suddenly soars in on a giant ice slide. He creates a gigantic icewall which literally crushes everything, including the devices disabling Xavier's telepathy. Free to use his powers, Xavier freezes every non-mutant mind in the area to buy time for his students. However, he is taken down by the Wasp, who is a mutant herself and thus passed over by the mind control. The X-Men flee, but Charles Xavier becomes a captive of Nick Fury.