X1: Professor Xavier acts as a physics and literature teacher at the school. During the Brotherhood's attack on New York, he was disabled by Mystique's sabotage of Cerebro and missed the entire event. Magneto has hinted that Xavier has some knowledge of Stryker's connections to Wolverine's past, yet this seems to contradict Xavier's surprise and revulsion of Wolverine's enhancements.
X2: While visiting Magneto in his plastic prison, Xavier (and Cyclops) were captured by Stryker and brought to Alkali Lake. Xavier was a critical part of Stryker's plan to wipe out mutants, using a Cerebro copy that Stryker had built. To get Xavier to use the machine, Stryker had his son Jason (Mutant 143), a powerful illusionist, project images into Xavier's mind, which was blocked from using his telepathy by a power inhibitor. At first Jason tried an illusion in which Xavier was walking, but clearly that was false enough to tip off Charles. Jason then appeared as a little girl in the mansion, and convinced Xavier to use Cerebro to find the missing students. Xavier proceeded to focus on all the world's mutants, Magneto nearly killing them. Magneto, who arrived with the X-Men, reversed the Cerebro effects to have Charles's power attack humans, but Xavier was rescued by Storm and Nightcrawler. Xavier then presented the President of the United States with detailed dossiers on Stryker's illegal activities, and implored him to promote human-mutant tolerance.
X3: Some time later, Xavier felt Jean's mind calling again, and dispatched Wolverine and Storm to find Cyclops, who had gone to Alkali Lake. When the X-Men brought Jean back to the school, but could not find Scott, Professor X was forced to reveal the psychic "surgery" he had done on Jean years before. After Jean escaped the school, Charles tracked her to her parents' house, where he tried to convince her to return with him, and not with Magneto, who had also arrived to claim her. Unfortunately, the Phoenix was in control, and she disintegrated Xavier. A large memorial was later erected in his memory on the school grounds.
Amazingly, Xavier managed to transfer his mind into the body of a man who was born with no brain functions, a patient of his colleague Moira MacTaggert. Only Moira knows about Xavier's survival at this point...
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