Several years in the future, mutants have been all but wiped out by giant robot Sentinels which can adapt to any of their powers. A small group led by Xavier and Magneto survives due to Kitty Pryde having developed the ability to send people back in time a few days, to alert them any time the Sentinels find them. Xavier has come up with a plan to erase the Sentinels from history by stopping Mystique from killing their creator Bolivar Trask in 1973, which is what convinced the world governments of their necessity, but only Wolverine will be able to survive such a long trip through time due to his healing ability. He is successfully sent back and quickly talks his way out of the job he had at the time.
In Saigon, Mystique infiltrates an army base disguised as a colonel and finds several mutants including Havok who William Stryker is about to take for his experiments. She fights off his men and gets them all into a helicopter, staying behind herself as she has more work to do.
Wolverine finds Xavier’s school in severe disrepair and only inhabited by him and Beast, who’s developed a formula that temporarily removes mutant powers and also enables Xavier to walk again. When the Vietnam War took most of the teachers and students, he retreated into a drug-fueled haze and initially refuses to help, though he eventually agrees for Mystique’s sake.
Mystique takes Trask’s form to get into his office, where she’s shocked to find the rest of her old team has been killed in his experiments, setting her on course to killing him. She heads to the peace summit in Paris where he’ll be speaking, and knocks out the Vietnam representative to take his place.
Wolverine’s first move is to free Magneto from a deep underground prison at the Pentagon, for which he recruits the speedster Peter “Quicksilver” Maximoff. The escape has a few hitches, but Quicksilver’s powers make short work of all the guards and soon the new team is on their own way to Paris, though Xavier and Magneto are still at each other’s throats.
Mystique reveals herself at the summit and is about to kill Trask when the team walks in, but Magneto goes rogue and tries to kill her so she won’t doom all mutants, ending up shooting her in the leg. Wolverine also sees Stryker in the room, which upsets him enough to become unstuck in time and accidentally injure Kitty before he can be put back, greatly decreasing how long she can hold him in the past.
Wolverine convinces Xavier to go off Beast’s drug so he can use his powers again to find Mystique with Cerebro. The first attempt is a failure as he can’t bring himself to face his self-loathing, but Wolverine allows their minds to touch so Xavier can talk to his older self, who helps him come to terms with his fear so he locates Mystique at an airport, and takes control of the people around her to talk her out of the murder. It doesn’t work, but he does see that she’s going to Washington DC where President Nixon and Trask are revealing the Sentinels to the public.
Magneto has made his own plans, slipping metal rods inside the Sentinels so he can control them, and getting his helmet back. When the presentation starts, he encases the White House inside a baseball stadium and turns the Sentinels on the crowd. Mystique disguised as a secret service agent slips into the building’s safe room with the others, but Magneto simply rips it out onto the lawn, and when Wolverine attacks stabs him with rebar and throws him in the river. Mystique turns into Nixon to distract him and is able to shoot him in the neck, after which Xavier is finally able to talk her down.
During the whole battle, the Sentinels also find the X-Men in the future, and most of them are killed protecting Kitty and Wolverine. But they manage to buy enough time that the mission is finished, and the entire timeline resets so that Wolverine finds himself in a new present where the School for the Gifted is still operating, plus Jean and Cyclops are still alive. In the past, Trask is arrested for colluding with foreign governments, and the contemporary Wolverine is recovered from the river by Stryker, but it’s revealed even this part of the timeline has changed as it’s really Mystique.
