The storyline is loosely based on the X-Men: Onslaught arc from the Marvel Comics continuity: following an incident in which mutant telepath Charles Xavier was forced to enter into the mind of Magneto, part of Magneto's anger slipped into Xavier's psyche, and after merging with Xavier's darkest emotions it spawned a powerful psychic entity known as Onslaught. The game expands on the story by having Xavier's conscience calling forth heroes from the Capcom universe in order to help stop him.

The storyline is loosely based on the X-Men: Onslaught arc from the Marvel Comics continuity: following an incident in which mutant telepath Charles Xavier was forced to enter into the mind of Magneto, part of Magneto's anger slipped into Xavier's psyche, and after merging with Xavier's darkest emotions it spawned a powerful psychic entity known as Onslaught. The game expands on the story by having Xavier's conscience calling forth heroes from the Capcom universe in order to help stop him.