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.
The four teams fight a losing battle against their horsemen, until Apocalypse moves his plan to the next level. The tops of the pyramids come off and line the Earth's atmosphere, connected to each other by some sort of energy. Pressed for time, the teams become desperate. The Brotherhood joins the team in Mexico to fight Magneto, and Jean amplifies her power with Cerebro to battle Xavier psychically. Apocalypse lies down in his original resting place, and the evolution of humankind begins. But in the last moments of the battle, Rogue shows up with Leech, and she takes his power and negates Apocalypse's power, ending the evolution before any harm is done. Apocalypse is shut into his machine and sent to another time period, and the horsemen fall out of their trances. Rogue and Kurt give Mystique the cold shoulder, and the episode ends with Xavier deeply disturbed after seeing glimpses into the future of the X-Men, and seeing Jean become the Phoenix, among other changes.
As all the monsters in the tomb attack, the teammates fight to survive and find a way out.
As Jean's and Scott's graduation day approaches, Rogue suddenly leaves the mansion.
Xavier starts worrying about the existence of mutants becoming public knowledge when the media starts reporting multiple sightings of a man with angel wings. With most of the X-men on Christmas leave, and Cerebro down for repairs, Scott and Rogue are left having to track the man down themselves.
Mystique escapes from imprisonment while the X-Men repair and rebuild the Institute. Disguised as Alex, she lures Scott into a trap - leaving him stranded in the middle of the Mexican desert without his glasses.
Forge is working on a device that will enhance Kurt's teleportation powers.
Rogue and Wolverine duck a squad of soldiers when the nationwide alert goes out against mutants, while Storm and Beast go into a meeting of Congress to defend themselves. Meanwhile Juggernaut goes on a rampage and the X-Men feel obliged to take him down.
Magneto steals the remaints of the top secret "Rebirth" project, a project Wolverine helped shut down all the way back in World War II.
The X-Men are on vacation with Storm as their guardian. Amara falls ill while on the ship.
After being grounded for reckless behavior during a training mission, Tabitha doesn't need her father showing up asking her to steal money for ""her mother""...
Wanda receives a clue from one of Magneto's minions, Pyro, directing her to a ski resort. Meanwhile, Kurt is meeting Amanda's parents for the first time, and the Toad believes he can use Kurt's holo-inducer to disguise himself and win Wanda's love.
A malfunction in Juggernaut's stasis field leaves the X-Men without adult supervision. Deciding to hold a party, they ditch Scott and Jean in the wilderness. However, things soon get out of control, when one of the guests gives himself access to Cerebro.
When a new sphere appears in Egypt, Professor X wants to try to communicate with Apocalypse, taking Storm with him. With Cerebro technology, the rest of the group watches as Apocalypse telepathically communicates his plan to awaken the dormant X gene in all humans, a process which will kill most 'normal' humans. Xavier tells Apocalypse that this isn't necessary, which angers Apocalypse. Storm comes to his defense, but instead sends them both away in the same way Magneto was. The X-Men are mortified, and are soon joined by Nick Furry who announces the restart of the Sentinel program. Apocalypse is confronted by three sentinels at the Sphynx, which act as decoys while more sentinels are sent to use their superior technology to disable the three spheres. Apocalypse defeats the sentinels, but sends out four horsemen under his control to protect them - Magneto in Mexico, Storm in China, Xavier in Egypt, and Mystique at the Sphynx. The X-Men split into four groups to fight the horsemen aroun
The X-Men and Brotherhood deal with the after math of the world finding out about mutants. Mystique, diguised as Professor X, manages to blow up the Insitute. Some of the X-Men and Brotherhood were captured, leaving the mutants that escaped to find them and the Professor.
When Jean and Amara feel like the boys think they are stronger than the girls are, Tabitha decides that they should form a girl's crime fighting club as the Bayville Sirens.
Evan enters an extreme Skateboarding competition, and puts his skills to the test. But something is wrong: A mysterious woman is watching and following him during the competition.
Mystique breaks a mysterious young girl out of an asylum and brings her to the Brotherhood House.
Jean has nightmares about huge circus clowns, then is controlled by the master of that circus, with Nightcrawler, Kitty, and Spyke controlled also.
Mesmero mentally controls Gambit into stealing half of the Spider Stone from Angel.
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, & Wolverine go to investigate. They try to be peaceful, but Magneto attacks. Apocalypse defeats him with ease, and appears to kill 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.
The kids get worried when the normally cool and collected teacher Hank McCoy starts having fits of animal rage.
Jean's abilities start growing in sudden bursts. At first she tries to ignore it, but with each burst she has increasing trouble regaining control. Meanwhile the school gets a new science/phys. ed. teacher.
Scott and Rogue end up on a geology club field trip together. Scott tries to be friendly to her, but it turns out Mystique has other plans...
Magneto reveals the his plans for the winners of his challenge - to fully unlock their powers with a machine he has built. Back at the mansion, those left behind regroup, and decide to pay Magneto a little visit.