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In ancient Egypt, the mutant En Sabah Nur, who thinks himself as a god, is burried in the middle of a body transfer process by a handful of rebels. In 1983, the tomb is dicovered in the middle of Cairo, and En Sabah Nur awakens. Discovering that people barely believe in gods (and in him) anymore, he decides to conquer the world. He gathers four disgruntled mutants (including Magneto, whose wife and daughter got accidentally killed by an angry mob) and travels to Xavier's school to abduct the professor, indirectly causing the destruction of the building. A handful of mutants are then captured by Stryker, while a small group manage to follow Stryker to his lair. There they free Wolverine who kills all the personel of the base. All the mutants are soon free and steal Stryker's prototype airplane to go to Egypt and save Xavier. The latter had been forced to broadcast a message from En Sabah Nur, stating that the apocalypse has come and tha only the strongest of the believers will survive. The mutants fight En Sabah Nur and finally vanquish him (not without causing massive amounts of destruction all over the world), thanks to Magneto, whom Xavier turned towards good once again. At the end, the X-Men are reforming, even though Xavier would have preferred not.

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In the near future, mutants are exterminated by invulnerable robotic creatures names Sentinels. They have been developed by Trask from the 1970s, and his assassination by Mystique in 1973 has convinced the government of the mutant threat and the need to eradicate them. Thanks to Kitty Pride's ability to send someone's mind back in time into ones own body, Logan wakes up in his 1973 body with the task, set by both Professor X and Magneto, to prevent Trask's death and the development of Sentinels. He manages to convince Charles Xavier of the veracity of his story and knowledge of the future, and thanks to the help of young Evan Peters they free Magneto from his cell in the middle of the Pentagon. The then track Mystique to the Vietnam War peace conference in Paris and prevent her from killing Trask, but she is wounded and thanks to her blood Trask manages to progress with Sentinel. During Traks presentation of Sentinel at the White House, Magneto flies a stadium around the building and uses the Sentinels to fire on the guards. He then extracts the saferoom containing President Nixon, his staff and Trask from the White House's basement and prepares to kill the President. Finally convinced by Xavier's arguments, Mystique prevents Magneto from doing that. Nixon is then convinced that mutants don't need to be exterminated, and Logan wakes up nowdays in his current body but in a new timeline; he and Xavier then exchange their knowledge of history since 1973.

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James Logan has a mutation that makes him immortal and gives him retractable claws. With his half-brother, also a mutant, they fight in all the american wars until the Vietnam war. James and Victor (and other mutants) are hired by Stryker as commandos to steal a mysterious meteorite, but Logan quits at the end of the operation, disgusted by the gratuitous killings. Six years later (in 1979) Stryker meets Logan in Canada and warns him that someone is killing the members of the mutant commando. Logan refuses to listen to Stryker and soon after his girlfriend Kayla is killed by Victor. When Stryker offers him a means to get his revenge on Victor, Logan accepts and becomes a subject in an experiment: infusing adamantium (an alloy created from the meteorite) into his skeleton to make it indestructible. The experiment is successful, but Loga ecapes when he overhears that Stryker plans to erase his memory. Chased by Stryker's men, Logan attempts to find “The Island” where Stryker's base of operations is locate; this happens to be hidden in Three Mile Island, below the nuclear powerplant. Logan discovers that his girlfriend is not dead, and that it was a ploy to convince him to participate in the experiment. Stryker then attempts to kill Logan through his last experiment, XI, a engineered mutant who has superpowers from many different, now-dead mutants. While Kayla helps all the mutants who are prisoner at the facility (and dies, for good, in the attempt), Logan, with the help from Victor, fight XI and provoque the famous catastrophe of Three Mile Island.