The plot revolves around Xavier, his past, discovering he is a mutant, and his relationship with his half-brother, Cain Marko. While Xavier discovered his gifts and grew into the man he is today, Marko went down an opposite path, seeking adventure and excitement. He ended up finding the Temple of Cyttorak and obtaining the Crimson Gem. Ultimately, he became the avatar of Cyttorak, which gave him great power but caused him to lose his mind, falling into a destructive rage. To prevent his brother from hurting more people, Xavier stops him.
Meanwhile, recent actions increase the hostile climate against mutants, raising many questions about the future of mutants and how far both mutants and humans would go in this confrontation. Senator Robert Kelly is one of the most active humans in this conflict, believing it will escalate into a war for the survival of one of the races. Manipulated by Mystique, he releases Marko, now known as Juggernaut, to go after the X-Men.
Taking advantage of the distraction created, Mystique, representing the Hellfire Club, goes after mutants to join her cause.
