Cylops leads the X-Men in a search for the missing Xavier and Wolverine.

The destroyed Institute is restored by the X-Men; Mystique escapes and sets a trap for Cyclops.

Rogue has no control over her powers, and the powers of others that she has absorbed surface, including those of Sabretooth, and the X-Men must find a way to help her.

Mesmero tries to free Apocalypse once again and uses Rogue to help him, while the X-Men join forces with Magneto and the Acolytes to stop him.