When Cyclops and Nightcrawler save people from a car crash they question Xavier's desire to keep their identities a secret. Meanwhile, the Brotherhood terrorize people in a crowded stadium.
Nightcrawler has a crush on a new student. The wild girl is grounded for breaking the rules, but things get worse when her father arrives and asks that she help him in a bank robbery.
Avalanche wants to join the Institute, but has trouble being accepted by the others, especially after he's accused of taking joyrides on the X-vehicles at night.
Jean is possessed by a mutant with telepathic powers, which he uses to control the students and have them help him in his plot to release the imprisoned Apocalypse, a mutant who wishes to enslave the human race.
Forge invents a teleporter, and Nightcrawler uses it to travel large distances, but inadvertently opens a portal that allows strange creatures to follow him back to the school.
Mystique frees a mutant called the Scarlet Witch from an asylum, hoping she'll help the Brotherhood, but Mystique doesn't know the witch is seeking revenge on Quicksilver and Magneto.
At Xavier's urging, the Brotherhood and the X-Men unite to battle Magneto; and the Institute begins to self-destruct while students are trapped in the mansion.