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.

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.

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.