Magneto and Joseph square off in the remains of Magneto's arctic citadel, wielding the massive electro-magnetic energies left in the wake of the Russian nuclear strike against Magneto.
Astra – a former disciple of Magneto and Joseph's creator – regards the destruction with glee. If Joseph's young, unchecked version of Magneto's powers prevail she will be one step closer to her goal of world domination.
Storm and Xavier pilot an Acolyte jet towards Magneto's base. Professor X senses the battle between Magneto and Joseph from miles away... and that Astra is watching from the sidelines. Wolverine is eager to enact revenge on Magneto, but it's Nightcrawler who makes the first move. Safe from EM interference in the eye of the global storm, he teleports to Sabra, snatches her, and dumps her into the icy landscape. Before he can port away, she taunts him in German, intimating that she has known him since his youth.
The X-Men split into two teams to contain Magneto and Joseph. Rogue leads the charge against Magneto, making an emotional plea for him to end his hostilities. Gambit ineffectually peppers Magneto with cards while Wolverine uses the distraction to try to punch his claws through Magneto's shields.
Meanwhile, Xavier lends the power of his psyche to Joseph, who is attempting the repair the Earth's magnetosphere. Colossus acts as a human conduit for the EM energies swirling in the air, which Storm is able to channel back into Joseph's body – serving to amplify his considerable power even more.
At the United Nations, Dr. Alda Huxley receives a report that the EM pulse wave deployed across the planet is beginning to recede. Seeing her window of opportunity beginning to close, she burns the report and rushes off to board a jet.
Magneto continues to hold the rest of the team at bay, but Nightcrawler relies on an old tactic and teleports away with Magneto's helmet. Wolverine uses the opportunity to deliver a brutal slash, yet Rogue prevents him from delivering a killing blow. Nearby, Joseph has managed to almost fully repair the Earth's magnetic field, but the effort has aged his synthetic body by several decades. Before Xavier can stop him, Joseph uses the last of his energy to finish healing the Earth and destroy Magneto's citadel. Joseph is vaporized in the process.
A bitter Astra briefly confronts the team and quickly ports away. Xavier reasons with Magneto, but he insists he will return to put the Earth in peril all over again. Before tensions between Magneto and the X-Men explode, they are interrupted by a United Nations envoy including Dr. Huxley and Magneto's servant Ferris. Dr. Huxley offers Magneto a proposal: he can rule over the sovereign state of Genosha as a mutant sanctuary.
Outraged, Wolverine launches himself at at the deliberations, but Xavier forces him to fall asleep. The X-Men skulk away from the diplomatic envoy, unable to watch as Magneto gets exactly what he wanted – a completely separate society for mutants.