Hank McCoy mad with grief over Raven's death, allies with Magneto and his team (including Ariki and Selene) in an attempt to kill Jean Grey in New York City. Upon learning of Erik's plan, the X-Men try to stop him and his faction of mutants. As they battle, Erik manages to enter the building and confront Jean, only to succumb to her amplified powers. Xavier then enters the building with Kurt Wagner. Jean attacks them until Xavier convinces her to read his memories – allowing her personality to resurface. Feeling remorseful, Jean offers to let Vuk take the force from her; however, it is revealed that doing so would kill Jean, as well as that Vuk intends to use the force to conquer Earth. Charles Xavier and Scott Summers are able to prevent Vuk from fully absorbing the force from Jean, though Jean loses consciousness from the ordeal. U.S. government troops using stun weapons and power-inhibiting collars attack and subdue both mutant factions, who are placed on a train headed towards a containment facility.
The train is attacked by Vuk and her D'Bari forces. When the soldiers are overpowered by the shape-shifters, the mutants are freed from their restraints to combat the threat. The mutants deal with most of the D'Bari attackers, but Vuk arrives and heads for Jean, defeating each mutant who attempts to stop her. Xavier confers with Jean within his mind, allowing Jean to gain control of her power. After forgiving Xavier, Jean saves the mutants from Vuk's attacks and the ensuing train wreck before proceeding to disintegrate the remaining D'Bari when they attack her. Vuk once again attempts to drain Jean of the force, but Jean takes Vuk into outer space, retakes the power that Vuk had received earlier, and then kills her. Jean then disappears in a burst of energy in the form of a phoenix.
In the aftermath of the incident, Xavier's school is renamed the "Jean Grey School for Gifted Youngsters", and Hank becomes the new headmaster with Xavier having retired. While settling himself in Paris, Xavier is reunited with Erik and agrees to play a game of chess with him. As they start playing, a flaming phoenix appears in the sky.