Magneto ruthlessly hunts Apocalypse, but the X-Men aren't so eager. When nothing can be done about Mystique, the professor gives her to the Brotherhood. Much to Rogue's objection, Kurt brings it back. When the two fight, Kurt sees a tear. Jean discovers Apocalypse in Mexico, and the professor, Cyclops, Jean, Shadowcat, Beast, and Wolverine go to investigate. They try to be peaceful, but Magneto attacks. Apocalypse defeats him with ease, and appears to hug him. Back in Bayville, Kurt has Wanda contact Agatha. Rogue finds the two meeting, and Agatha tells her that she's the only one who can save her mother. Kurt begs her to do the right thing, but Rogue knocks the statue off the cliff. It shatters before Kurt can teleport down to it, and Rogue just walks away.
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.