In a dystopian future, robots known as Sentinels are exterminating mutants and oppressing humans who harbor the genes that lead to mutant offspring. In an underground bunker in Moscow, a small band of mutants manage to evade the Sentinels due to Kitty Pryde, who can project a person's consciousness back in time.
Pryde's group rendezvous with Storm, Wolverine, Professor Xavier and Magneto in a Chinese monastery. They decide to send Wolverine's consciousness back to 1973 to prevent Mystique from murdering Bolivar Trask, the designer of the Sentinels. The assassination will make Trask a martyr, Mystique will be captured, and her mutant powers will be reverse-engineered and used to create the formidable Sentinels of the future. Xavier advises Wolverine to seek out his and Magneto's younger selves for aid.
Wolverine wakes up in 1973 and travels to the X-Mansion, where he encounters Xavier and Hank McCoy. Xavier's Institute for Gifted Youngsters is closed, most of the students have died in the Vietnam War, and Xavier has become a broken man. He has also lost his telepathic powers, due to a serum that allows him to walk. Wolverine persuades Xavier to free Magneto from a prison cell beneath The Pentagon. They enlist Peter Maximoff, a mutant with superhuman speed, to assist them.
Trask unsuccessfully lobbies his Sentinel program to Congress. In Saigon, Mystique prevents a young William Stryker from appropriating a group of mutant GIs for Trask's research. Mystique investigates Trask and discovers he has been capturing and experimenting on mutants. Xavier, Magneto, Beast, and Wolverine go to intercept Mystique in Paris.
In Paris, the Americans and Vietnamese are negotiating the end of American involvement in the Vietnam War. Mystique impersonates a general to infiltrate a meeting with Trask. Xavier, Magneto, Beast, and Wolverine arrive as she is about to kill him. Believing that the dark future can only be avoided through Mystique's death, Magneto shoots at her; she flees, wounded by the bullet. The ensuing altercation exposes the mutants in front of onlookers and television cameras. Wolverine's encounter with Stryker causes his future body to react violently, injuring Pryde.
Although Trask is saved, the world is horrified by the existence of mutants. President Richard Nixon approves Trask's Sentinel program and arranges an unveiling in Washington, D.C. Trask's scientists recover Mystique's blood from the battle site in Paris, allowing him to research further Sentinel improvements. Magneto intercepts the Sentinel prototypes and laces their polymer-based frames with steel. At the mansion, Xavier stops taking his serum and regains his powers. Through Wolverine, Xavier speaks to his future self and is inspired to struggle for human-mutant peace once again. He uses Cerebro to track Mystique, who is going to Washington.
Nixon unveils the Sentinel prototypes on the White House lawn. Magneto raises the Robert F. Kennedy Memorial Stadium and places it around the White House as a barricade, then commandeers the Sentinels and attacks the crowd. Nixon and Trask are taken to a safe room, followed by a disguised Mystique. Xavier, Wolverine, and Beast try to stop Magneto, but he impales Wolverine with rebars and throws him into the Potomac River. In the future, the Sentinels kill most of the mutants.
In 1973, Magneto pulls the safe room out of the White House and prepares to kill Nixon. Mystique, disguised as Nixon, shoots Magneto, and Xavier persuades her not to kill Trask and lets her and Magneto flee. The Sentinel program is cancelled and the dystopian future is averted. Trask is later arrested for selling military secrets.
Wolverine wakes up in the future at Xavier's school, where he finds Iceman, Rogue, Colossus, Pryde, Beast, Storm, Jean Grey, Cyclops, and the older Xavier alive. In 1973, Mystique, impersonating Stryker, rescues Wolverine.
In a post-credits scene, a multitude of people gathered in the desert bow and chant while a cloaked En Sabah Nur uses telekinesis to construct a pyramid as four horsemen stand behind him.
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