In a San Francisco divided into separate human and mutant districts by rising conflict, the story begins at a peace rally held in memory of the recently deceased Professor X. The player takes on the role of one of three brand-new mutants, Aimi Yoshida, Adrian Luca, or Grant Alexander, whose latent powers suddenly awaken when the rally is attacked by the Purifiers, an anti-mutant extremist group that has begun abducting mutants rather than killing them. Forced to fight back and protect the civilians caught in the chaos, the young mutant soon crosses paths with both the X-Men and the Brotherhood of Mutants. As the crisis deepens, the choices the player makes will determine which side they stand with and which mutants become their allies or enemies.