As the Beast faces an arraignment in court before a mutant-hating public, the X-Men unwillingly take in an old enemy of Wolverine's. Magneto, an old friend turned enemy of Professor Xavier's, attacks a military base in an attempt to unite mutants against humanity.

Wolverine must overcome his feelings for Jean, and Storm must overcome her crippling claustrophobia, when the team journeys into the sewer to rescue Jean Grey & Cyclops from a race of hideously deformed mutants known as Morlocks, and their leader Callisto, who wants to make Scott her king