Before Charles Xavier and Erik Lensherr took the names Professor X and Magneto, they were two young men discovering their powers for the first time. Before they were arch-enemies, they were closest of friends, working together with other mutants (some familiar, some new), to stop the greatest threat the world has ever known.

After seeking to live a normal life, Logan sets out to avenge the death of his girlfriend by undergoing the mutant Weapon X program and becoming Wolverine.

When a cure is found to treat mutations, lines are drawn amongst the X-Men—led by Professor Charles Xavier—and the Brotherhood, a band of powerful mutants organised under Xavier's former ally, Magneto.

Professor Charles Xavier and his team of genetically gifted superheroes face a rising tide of anti-mutant sentiment led by Col. William Stryker. Storm, Wolverine and Jean Grey must join their usual nemeses—Magneto and Mystique—to unhinge Stryker's scheme to exterminate all mutants.

Two mutants, Rogue and Wolverine, come to a private academy for their kind whose resident superhero team, the X-Men, must oppose a terrorist organization with similar powers.