It is a bleak future for mutants, hunted by highly-advanced Sentinels. A small group of X-Men are mutantkind’s only hope. To save their future, Kitty Pryde sends Wolverine’s consciousness back in time to 1973 to prevent the assassination of Bolivar Trask, the creator of the Sentinels. The assassin, Mystique, was captured after the fact, and her mutant ability was harnessed to improve the Sentinels.
Xavier and Magneto of the future advised Wolverine to find their younger selves to aid in his quest. But it proves to be a tall order for Wolverine. He finds the younger Xavier disillusioned, and the younger Magneto imprisoned for the alledged assassination of President Kennedy. Wolverine persuades Xavier and Hank to free Magneto, with the help of Pietro Maximoff.
In Washington D.C., Trask is unsuccessful in gaining support for his Sentinel program from Congress. Mystique discovers Trask has been capturing mutants and experimenting on them. She plans on killing Trask at the Paris Peace Accords, disguised as a North Vietnamese general in attendence at Trask’s sale of Sentinel technology to the world’s communist nations. Xavier, Magneto, Hank and Wolverine manage to foil Mystique’s plans. But in the process, they reveal the existence of mutants to the world.
The world is horrified, and this pushes President Nixon to approve the Sentinel program. The Sentinels are scheduled to be unveiled. Magneto devices a plan to intercept and control the Sentinels. Xavier stops taking his serum, trading in his ability to walk and regaining his telepathy. Through Wolverine, Xavier corresponds with his future self and that restores faith in his work for peace between humans and mutants.
Mystique is determined to carry out the assassination at the unveiling. Xavier, Hank and Wolverine track her to Washington D.C. After the Sentinels are unveiled, Magneto controls them to attack the crowd, and then drops the Robert F. Kennedy Memorial Stadium around the White House to barricade it against the police. Nixon, Trask and the Cabinet are taken to a safe room by the Secret Service. Mystique is disguised as one of the Secret Service officers.
In the future, the X-Men are preparing for their last stand against the Sentinels.
Back in 1973, Wolverine and Hank try to stop Magneto, but are overpowered. Magneto then rips the safe room from the White House and is about to assassinate everyone in the room. Mystique, now disguised as Nixon, uses a plastic gun to stun Magneto. Xavier is able to persuade Mystique to spare Trask’s life. He also allows Mystique and Magneto to escape. Mystique is deemed a heroine for saving the President’s life, and her actions put mutants in a good light. President Nixon cancels the Sentinel program. Trask is arrested.
Wolverine wakes up in an altered future. He finds his friends and X-Men, who had otherwise died, alive and well. Walking the school’s bustling halls, he finds Iceman, Rogue, Colossus, Kitty, Hank and Storm, surrounded by many students. As he approaches Xavier’s study, he is shocked to see Jean alive. When he reaches out to touch her, a hand grabs his to stop him. Scott is alive as well, and Wolverine is overjoyed, leaving Scott slightly confused regarding Wolverine’s friendly demeanour towards him. Scott takes his leave, not before telling Wolverine to mind himself around Jean, just like old times. Wolverine spends some time catching up with Xavier.