The past history of Charles Xavier of Earth-21993 would mirror his Earth-616 counterpart up until the point in which he was captured by the Skrulls to be used as a weapon against the Shi'ar empire. Returning to Earth, Xavier would find human mutant relations in complete chaos. Freeing Havok from Genoshan brainwashing, restoring Colossus, Dazzler, and Psylocke from their amnesia and driving off the Shadow King from Muir Island, Xavier would call together the X-Men, X-Factor and the New Mutants to call them to task for the state of the world.
This would lead to an ideological clash with the New Mutants mentor Cable who believed that they should strike at their enemies instead of pandering to humanity. This argument would devolve to Xavier demanding that Cable be taken away from the New Mutants, leading to a clash between the Mutants and the X-Men. With the Mutants and Cable escaping, Xavier would attempt to wipe out Cable's mind and fail. Cable vowing to Xavier that if he wants to go to war with him, he'll get it. Shortly thereafter, Xavier would meet with Cyclops and Marvel Girl to figure out strategies to boost humanities opinions on mutants when they would be attacked by Cable, who would assassinate all three of them with a bomb.
Xavier's death would spark not only the X-Men splitting into two ranks, but cause widespread mutant terrorist activities perpetuated by the X-Men's various enemies, and the eventual conquering of the United States by the mutant hunting Sentinel robots.