At the end of a war between the Avengers and X-Men, Cyclops was possessed by the Phoenix and murdered his mentor, Charles Xavier, in a fit of rage. Xavier is gone now, but he’s still very much at the center of stories. His brain was stolen by the Red Skull, who grafted it to his own, granting the evil Nazi immense psychic powers. An evil young man from the future who looks just like Xavier and has the same powers was revealed to be his son with Mystique. When the X-Men had to come together for the reading of his will, it was revealed that Xavier was in fact married to Mystique, and that he had essentially lobotomized an immensely powerful mutant named Matthew Malloy and kept him a secret from the X-Men. Where to start: For his death, Avengers Vs. X-Men, and for "The Last Will and Testament of Charles Xavier," Uncanny X-Men Vol. 4: X-Men Vs. S.H.I.E.L.D.
Marvel Comics