The full story
One year after Professor Xavier left Earth with the Shi'ar, the X-Men are still adjusting to his absence — and to his will, which hands control of the team and the school to Magneto. At Magneto's UN trial for his own past crimes, the anti-mutant Friends of Humanity attack and Storm loses her powers protecting him. Jean Grey gives birth to a son, Nathan, who is kidnapped by Mister Sinister and infected with a techno-organic virus; Bishop takes the infant into the future to find a cure. A clone of Jean, Madelyne Pryor, surfaces and is manipulated into becoming the villainous Goblin Queen before breaking free on her own.
At a celebration in Genosha, the mutant nation Magneto has been building, an adult version of Nathan arrives from the future calling himself Cable — and vanishes again before he can finish warning the team what's coming. What's coming is an upgraded Master Mold and an army of Sentinels, which massacre thousands of mutants in Genosha; Gambit dies destroying the Master Mold. Xavier, who refused to give up his memories of Earth during a Shi'ar ritual, returns from space to find his life's work in ruins.
The attack turns out to be the work of Bastion, a human-machine hybrid using Sinister's stolen techno-organic virus to convert ordinary humans into Prime Sentinels, backed by a secret UN program called Operation: Zero Tolerance. When the Prime Sentinels activate worldwide, Magneto triggers a global blackout that kills thousands of humans to disable them, then retreats to his orbital base, Asteroid M. The X-Men split in two: one team goes after Magneto, while the other goes after Bastion and Sinister.
Jean channels the Phoenix Force to strip the Prime Sentinels' programming and restore their humanity. Wolverine, believing Magneto beyond redemption, stabs him — and Magneto rips the adamantium out of Wolverine's skeleton in response. Xavier takes control of Magneto's mind to end the fight and restore the power grid, but the effort fractures Magneto's own sanity. The U.S. launches a missile strike on Asteroid M anyway; Magneto flings it out into space, where it detonates, and the X-Men are presumed dead.
Six months later, Bishop reveals what actually happened: the team was scattered through time in the blast. Cyclops and Jean land in the year 3960, where they meet the future Askani order and a grown-up Nathan. Rogue, Nightcrawler, Beast, Xavier, and Magneto land in Egypt in 3000 BC, where a young En Sabah Nur finds Gambit's playing card among their wreckage — a sign of the villain he's destined to become.