In the year 2055, New York City is in ruins. Sentinels are chasing after an aged Wolverine and and two younger mutants. These three are considered “rebel” mutants, and they are taken out by another mutant, whom we know later to be Bishop. Wolverine and the others are taken to a camp facility. By becoming a “tracker” Bishop assumes that his life will be spared in exchange for the capture of other mutants. But the Sentinels overrule Bishop’s rights because he is a mutant and sends him off to be exterminated along with the others he helped capture.
Wolverine comes across the burial ground of his fellow X-Men in the camp. Seeing the gravesite of Jubilee, the kid who Wolverine had grown fond of, pushes him over the edge. He starts attack the Sentinels. Bishop comes to Wolverine’s aid. The normal Sentinels are taken down easily, but Nimrod arrives. We learn that Wolverine is on a special mission.
Wolverine, with Bishop, deliver a special package to a mutant named Forge, that enables Forge’s “time portal” to function. Wolverine intends to travel back to the 90s to prevent the assassination of Senator Kelly. Bishop wants to go in Wolverine’s place, stating two reasons: one being Wolverine’s age, and two being Bishop’s unbiasedness towards the X-Man he is supposed to kill to prevent the assassination. Forge agrees with Bishop’s reasoning. Bishop makes it into the time portal just as the Sentinels arrive.
Bishop arrives in the past, but has no recollection of who he is or what he is supposed to do. Chancing across a headline regarding Professor Xavier, Bishop decides to seek Xavier.
Rogue and Gambit pay a visit to Beast in his prison cell. Gambit doesn’t take a liking to being imprisoned in a small space and takes his leave. Beast speculates that in Gambit’s past, he must have been held a prisoner before.
Bishop hides in an abandoned building, and watches recorded footage about the X-Men on his “temporal transceiver”. A couple of kids run past him talking about a video game called Assassin. This triggers Bishop memory partially, until his transceiver tells him he has to “take out” the X-Men.
Bishop hijacks a bus and rams it into the mansion. He immediately starts firing at the X-Men he sees. Bishop is ambushed by Wolverine, whom he recognises. Xavier comes in to break up the fight. With the help of Cerebro, Xavier catches a glimpse of the dark future via Bishop’s transceiver.
Cyclops and Wolverine are still sceptical about Bishop’s claims. Suddenly, the transceiver sets off an alarm, meaning that “something or someone has come through the time portal”. The X-Men and Bishop check out the area where “temporal displacement” took place. They discover that Nimrod, “the new Sentinel of the future” had followed Bishop into the past. Together, they manage to blast Nimrod into pieces, leaving Bishop enough time to destroy Nimrod’s temporal transceiver, sending Nimrod back into the future.
Back at the mansion, Wolverine wants Bishop to point out to them the assassin among them. Rogue and Gambit return from visiting Beast, and Bishop jumps up at the sight of Gambit, declaring him to be the assassin.