The game is based on the current story arc from the comics at the time of development. The plot is narrated through the Cerebro and Professor X's communication with each other. Cerebro detects that the technorganic alien race known as the Phalanx have returned and have contaminated a sentinel manufacturing facility. Learning this, Professor X sends the X-Men (Beast, Psylocke, Gambit, Nightcrawler, Wolverine, and Cyclops) to destroy the Phalanx virus, but discovers that the virus has spread to Avalon, home of Exodus and Magneto. Magneto then allies with the X-Men in preventing the Phalanx from taking control of Earth by assimilating all of its inhabitants. They trace the Phalanx to Apocalypse's facility, where he has allowed the virus to spread. After defeating him, they leave to the Savage Land where they defeat a Phalanx clone of Brainchild who was overseeing the assimilation. They continue to the Phalanx ship where they are attacked by Deathbird, and then proceed to the clone factory and the Nexus before confronting Phalanx clones of themselves.