A clandestine government operation led by military scientist William Stryker begins to target the mutant community, inciting fear and distrust among humans and mutants alike. Stryker, obsessed with eradicating mutantkind, launches an attack on Professor Charles Xavier's School for Gifted Youngsters. This aggressive act forces the students to flee, while the professors and veteran mutants band together to understand and counter the imminent threat that Stryker poses. Meanwhile, Stryker has a personal vendetta against the mutants and possesses a deep connection to Wolverine's mysterious and turbulent past.

As Stryker's plan becomes more evident, it compels the mutants to form unlikely alliances for their survival and the protection of those they hold dear. Magneto, previously an adversary, finds a common cause with Xavier's team in facing the human threat led by Stryker. Together, they must confront the escalating conflict, prevent a potential genocide, and deal with their own internal battles of prejudice and acceptance. As they venture deeper into this struggle, the mutants begin to uncover the full extent of Stryker's scheme, which could not only destroy their lives but also the very fabric of peaceful coexistence between humans and mutants.