Loosely following the main stories from the original comic, X-Men: Evolution accompanies the lives of six mutants (Cyclops, Jean Grey, Nightcrawler, Shadowcat, Rogue, and a new original character named Spyke) who attend Xavier's Institute for the Gifted, where they ought to learn how to control their powers and use them for good.

These teenagers must face a world that both fears and despises them.