In May 2003, Xavier's School for Gifted Youngsters was attacked by a government-sanctioned military group led by William Stryker - Phase 1. In the chaos, some residents were captured and relocated to Alkali Lake, whilst others escaped and holed up in various safe houses and hotels, trying to reach their compatriots and work out a plan. With Charles Xavier and Scott Summers among the missing, this was difficult. Stryker, a Vietnam veteran and scientist whose experience of mutants had left him bitter and hostile saw Charles' refusal to 'cure' his son Jason of his illusion power as an attack and following the death of his wife due to their son's powers, he vowed to wipe out all mutants, using a bastardised version of the Cerebro technology and Charles Xavier himself.
Jean Grey, Ororo Munroe, Logan and new recruit Kurt Wagner formed an uneasy alliance with Magneto, recently freed from prison by Mystique. Retrieving Logan, Marie D'Ancato, Bobby Drake and John Allerdyce from near-arrest at Bobby's parents' house, they used Kurt's memories of Stryker's base from the time he had been abducted and brainwashed into attacking President McKenna to find the base underneath a dam at Alkali Lake. and began a rescue effort.
In the battle, Jean fought with a brainwashed Scott, and the impact of their battle weakened the structure of the dam, causing it to begin to leak. Logan disappeared to pursue his past with Stryker, who used his bodyguard 'Lady Deathstrike' to delay him enough to attempt escape. After a fierce fight, Logan killed the brainwashed mutant with molten adamantium and continued the pursuit, finally catching up with Stryker but not killing him despite taunts about his 'animal' nature.
Manipulated by Jason's illusions, Charles was encouraged to use his telepathy, amplified by Cerebro, to seek out all mutants on the planet and kill them. Magneto, however, had other ideas, and used Jason's confusion and Mystique's shapeshifting to convince him to use Charles' power instead to kill all humans. He and Mystique then fled, stealing Stryker's helicopter and leaving the man chained to the base. John, disillusioned with the way mutants had been treated by humans, went with them. After a blind teleport by Kurt, he and Ororo managed to stop Jason and rescue Charles as the bases began to collapse from the impact of Scott and Jean's battle. A last-minute save by Marie in the Blackbird gave them some hope, but engine failure prevented them from taking off immediately. It was then the dam fully collapsed.
Jean, realising that her recently-amplified powers were the only thing that could save everyone, left the plane and held back the wall of water long enough for them to take off. Once her comrades were clear, she released her telekinetic hold and appeared to perish beneath the flood, along with Stryker.