Charles Xavier is a psychiatrist who ran the "Xavier School for Exceptionally Wayward Youth", in Westchester where he took in juvenile delinquents. But instead of reforming his students, he actually further trained them in criminal talents, due to his belief that sociopathy was in fact the next state in human behavioral evolution. The paper in which he stated this led to his expulsion from the American Psychological Association. Xavier was arrested and incarcerated in Rikers Island, after his unorthodox teachings were made public following the death of one of his students Warren Worthington III, caused by Xavier's friend Eric Magnus when Xavier refused to make his "X Men" to join the Brotherhood.

Months after the death of Magnus and all the other people who testified against Prof. Xavier, Xavier was released on this technicality and having sworn that he is innocent and claimed to want to avenge Mangus' death. Xavier created a new X Men and worked with the Office of National Security (O*N*E*), in helping recruiting a new generation of government operatives at Genosha Bay. He later approached his freed stepbrother Cain Marko in retrieving the Gem of Cyttorak in order for O*N*E* to bargain the gem with Prince Baran for relocating Genosha Bay's operations to a piece of territory in Madripoor. However, Cain reneged Charles' deal by having the gem hidden and demanded to be handsomely paid for the gem. Charles oversaw O*N*E* in apprehending Cain and then having him killed by dumping him from O*N*E*'s Dirigi-Carrier in mid-air, sending him falling to his death, in order to draw out Thomas Halloway, who have knowledge of the gem's location.

After capturing Holloway at Genosha Bay, Xavier tortured him through Project: Wideawake in seeing to his own purpose of studying on his new theory of "heropathy" which he saw in him when they first met at Rikers Island. By doing so he wanted to see if Thomas would become more of his sociopathic brother Robert Halloway. At first Charles' experiment made him to thought that Thomas' psych fell to his brother's persona, but at the last moment was tricked into revealing his responsibility for Cain's murder and then suddenly arrested by FBI agents.

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