It begins in the future, where Sentinels fly by a dilapidated statue of liberty. Wolverine leads two other mutants through the abandoned streets of New York. One, a female, has the ability to shoot forceful, concussive blasts from her hands. The other, a male, can turn his arms into steel akin to Colossus. Suddenly, two Sentinels emerge from the nearby buildings. Wolverine seemingly disappears, but his companions make short work of the robots. A third Sentinel lands unexpectedly, but just as surprisingly topples over with Wolverine plunging his claws into its back. Wolverine comments that he is getting rusty in his old age.

A tracker named Bishop appears, agrees with Wolverine, and then apprehends all three mutants after a brief skirmish.

On the way to a mutant termination center, Wolverine regains consciousness; and from his bondage, discusses politics with his captor Bishop. Bishop insists that “the rebels” (like Wolverine) would be all right if they would stop attacking the Sentinels. Wolverine argues that the Sentinels want to kill all mutants and will eventually betray trackers like Bishop.

When they reach the termination center, the Sentinels do turn on Bishop and declare all four mutants are to be killed. Wolverine gloats about being right. Logan and Bishop (each carrying one of Wolverine’s unconscious companions) are escorted by the Sentinels. They pass by the tombstone of the legendary X-Men.

The female mutant awakens and blasts one of the unsuspecting Sentinels. Wolverine and Bishop destroy the other. Then Nimrod, the perfected Sentinel, arrives. Wolverine prepares to fight, but his female friend reminds him of “the mission.” The male and female stall Nimrod as Wolverine and Bishop escape.

Wolverine and Bishop arrive at a rebel hideout. Logan introduces Bishop to Forge who is working on his time portal. As Forge prepares Wolverine for his time travel, he explains the rebels’ theory to Bishop. If the assassination of the 1990’s never occurred, then none of the Sentinels, death camps, or terminations would have occurred either.

Wolverine instructs Bishop to destroy the time portal after he jumps through. He does not want anyone or anything following him in. Logan elaborates that he will stop the assassination by killing the triggerman. Bishop realizes the ramification of Wolverine’s words, and he replies, “You couldn’t handle me. How are you going to stop an X-Man?”

Forge sees the truth in Bishop’s statement and suggests that he go instead. When Wolverine protests, Forge insists that Bishop will get all his information that he needs from his temporal transceiver – a wristband that will also maintain him outside of his time.

Bishop jumps into the time portal as Sentinels arrive. He sees Nimrod follow him, and then he finds himself in a strange alley. Observing the ruins around him, he thinks he is still in his own time instead of the late twentieth century.

Bishop begins to see suspicious things, like children playing in the street during daylight. His suspicions are confirmed when he sees a newspaper. Oddly, Bishop’s landing in the alley has turned him into an amnesiac. He cannot remember why he came back in time. A closer look at the newspaper reveals that Professor Xavier is on his way to Washington to give a speech. Bishop decides that he is here to see Xavier.

In addition, in the present, Gambit and Rogue are visiting Beast in prison. While Beast jokes about his incarceration, Gambit is noticeably uncomfortable. Eventually, he insists on waiting outside. Beast suggests to Rogue that Gambit might have a history of imprisonment.

Elsewhere, Bishop uses his transceiver to piece together his mission. He realizes that he is in the past to stop an assassination, but he cannot remember of whom. Moreover, he remembers that one of the X-Men is supposed to be the murderer, but he cannot remember which one. Bishop departs for the Westchester mansion, by bus no less.

At the time, Jubilee is watching the mansion’s defenses, and she observes the “creepy dude” coming. It takes the combined efforts of Cyclops, Storm, Wolverine, and Jubilee to eventually bring Bishop down; but when Wolverine goes to finish him, Bishop calls him by name and claims that he has to do this for the future.

Wolverine is unmoved, but Professor X calls them off claiming that Bishop’s death would not answer any of his questions.

In the war room, Cyclops and Jean Grey analyze Bishop’s weaponry as the others hook Bishop up to Cerebro. Jean observes that the weapon is unlike any she has seen.

Professor X begins reading Bishop’s mind and simultaneously projecting it on a monitor for all the X-Men to see. Storm correctly identifies these visions as the future, but Wolverine thinks Bishop is a fraud. Jean insists that his feelings are genuine. Professor X then sees the disturbing vision of the X-Men’s clustered tombstones. Xavier sadly declares, “We have failed.”

Wolverine continues to deride Bishop’s claims when the temporal transceiver begins beeping. This means someone or something has followed Bishop through the time portal and is now in the present (or past, relatively).

Xavier decides that he will believe Bishop tentatively, and the X-Men must assist him, even if that means stopping one of their own. Wolverine responds by declaring himself Bishop’s personal baby-sitter.

The X-Men (Cyclops, Storm, Jubilee, Wolverine, and Jean) and Bishop go to the place of the temporal disturbance. Unexpectedly, Nimrod attacks them. As Bishop explains who Nimrod is, the X-Men are summarily defeated. That is, until Storm manages to freeze it and Bishop blasts it apart. Nimrod attempts to rebuild itself, but Bishop shoots its temporal transceiver sending it back to the future.

Back in the mansion, Wolverine demands to know who the assassin is. Bishop insists that he cannot remember. Cyclops replies that it could not be Jean, but Storm remarks that it could be anyone. “We all have our dark sides,” she observes.

Finally, Rogue and Gambit return from their visit. Bishop recognizes Gambit immediately… as the assassin.