To fulfill his father, Xavier’s dream of co-existence between humans and mutants, Legion travels back in time and kills a younger Magneto. But in the course of doing so, Magneto wasn’t alive to save his mother, Gabrielle Haller and she dies. Subsequently, Legion would not be born in this lifetime.
In the present day, Xavier browses through the morning’s news. He broods on how mutants have become “freaks and entertainers, doing television tricks in return for an ounce of acceptance”. In the Danger Room, Forge is training the X-Men in a choreographed rehearsal against the Hellfire Club as entertainment for a speech Xavier is giving at the White House. It seems that Forge is now running the X-Men, while Xavier is merely a spokesperson for the organisation. Forge’s plan was to have the rivals X-Men and the Hellfire Club fight then make nice to “publicly quell the rumours of bad feelings between [them]”. The X-Men are defeated at 60% of the stimulated Hellfire Club’s capability. The idea doesn’t sit well with Xavier, but it is Forge who calls the shots.
Meanwhile at the Hellfire Club, Sebastian Shaw is discussing business with the Inner Circle. Warren Worthington and Bobby Drake have quit the X-Men and defected to join the Hellfire Club. Suddenly there is an explosion and the Hellfire Club is massacred by a group of rogue mutants. Behind this staged attack is Apocalypse, who is on a mission to “cull” mutants who are “inadequate”.
Charles Xavier has travelled to Anchorage, Alaska to see his former students, Scott and Jean Summers. The couple are now happily married and settled with their children, Nathan and Rachel. Both Scott and Jean had resigned after Jean’s acquiring of the Phoenix Force. Their confrontation with the Hellfire Club saw Warren and Bobby’s defection. Xavier has come to ask Scott and Jean to join his mission, but Jean flatly refuses, stating that the last mission they undertook was a disaster. Scott had made a promise to his wife, and thus reluctantly but firmly refuses Xavier.
A few days later, Xavier addresses a crowd in Washington D.C.. Suddenly, unidentified figures fall from a mysterious spacecraft above them. Xavier senses danger and warns his X-Men that it is not a stunt and to prepare for a real battle. The attackers fire guns, and Xavier reaches out with a “desperate psychic command” putting majority of the crowd to sleep, but not the attackers. Apocalypse appears from amidst the smoke, and threatens Xavier’s life.
Back in Alaska, Scott and Jean witness the carnage broadcast on television. Silently, they know what they must do. Biding their children goodbye, and assuring them they wouldn’t be gone long, Jean summons the Phoenix Force again, dressing her and Scott in their old X-Men uniforms and transports the couple to Washington D.C..
Cyclops and Phoenix attack Apocalypse with full force. Cyclops tries to rescue Xavier, but Xavier unleashes one last psychic attack on Apocalypse, the result killing both Xavier and Apocalypse. Apocalypse’s goons attempt to regroup and retreat, but Phoenix would not see to that. She summons her phoenix powers and in one explosion kills everyone in D.C.
A few months later, Washington D.C. is still in flames. Conspiracy theories are rampant, and there is great hatred directed at mutants. Jean Summers watches the news, regretting her actions.
But on a brighter note, Scott and Jean Summers have moved back to Westchester with their children and reopened the Xavier Institute to mutants to help them “learn more about themselves and to show them all their futures”. Scott Summers intends to carry on Xavier’s dream.