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. Though, when Cain instead hidden the gem and wanted to be paid handsomely for the Gem, he was arrested by O*N*E*. Xavier oversaw his stepbrother and had 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. 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 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 being responsible for Cain's death and then being suddenly arrested by FBI agents for the murder.
- This version of Professor Xavier bears some similarities to Hugo Strange.