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Charles Xavier's life changed when his son Legion traveled to the past and killed Charles' would-be friend Magneto, due to Magneto's absence, Charles was unable to save Legion's mother Gabrielle when she was kidnapped by HYDRA, thus erasing Legion from existence.

Charles eventually formed the X-Men and led the team towards the goal of coexistence between mutants and humans.

The X-Men reached their goal after some time and became media heroes. Charles was worried about the state of the team, thinking that the X-Men were reduced to freaks and entertainers, doing television tricks in return for an ounce of acceptance. He was also worried about strange mutant presences discovered by Cerebro, but his superior, Forge, ignored his premonitions.

Xavier went to Anchorage, Alaska to recruit the help of former X-Men Cyclops and Jean Grey, who were married and had two children, but they refused as they felt that being an X-Man was to be dead or a freak show.

The X-Men were then attacked and almost slaughtered by the Followers of Apocalypse, and Xavier eventually went to challenge the villain responsible for the attack, Apocalypse himself.

Apocalypse appeared and lifted Xavier out of his hoverchair, Charles tried to fight back mentally, but Apocalypse stated that both his overwhelming power and vast vestments were blocking/damping Xavier's from affecting him or his followers. Apocalypse was about to run Xavier through, until a Phoenix Force empowered Cyclops striked Apocalypse down, giving Jean, who was also empowered by the Phoenix Force, the chance to pull Xavier away with her telekinetic powers. Jean then passed Xavier to Cyclops, who was trying to fly Xavier to safety. Unfortunately Cyclops was hit by a gataling plasma rifle shot by one of Apocalypse's followers called Gideon, which caused Cyclops to drop Xavier to the ground.

While Apocalypse was fighting Jean, Xavier managed to crawl his way behind him. In that moment Charles Xavier used the last inch of his power to finally break into Apocalypse's mind and stamp on it, causing both Apocalypse and Xavier to die.

After his death, Phoenix took out Apocalypse's troops, destroying most of Washington in the process. Jean and Scott took over the school, raising a new mutant generation in a now more hostile climate.

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