Mystique sees an opportunity to get a spy in Xavier's institute when the morally shady Todd Tolanski starts exhibiting mutant powers. Kurt Wagner, Xavier's latest recruit, arrives and tries to familiarize himself with his new life as part of the X-Men.
15-year-old Kitty Pryde wakes up one day and finds herself able to walk though objects. She tries to ignore it, but finds that hard when she's approached by Jean Grey and a mutant trouble maker, who both say they know what she's going through and want to help her. Meanwhile Wolverine's old nemesis, Sabertooth, arrives in town - looking for trouble.
After being kept in the dark about her powers for years, a young female mutant touches a fellow student and absorbs his strength, his memories - his life. Afraid and confused, and unable to differentiate her memories from the absorbed ones she runs away - straight in to the hands of Mystique.
The only thing bigger than Fred Dukes' strength and size, is his temper, which makes his first day at school rather difficult. When Jean Grey makes contact, trying to be friendly, he takes it just a bit too seriously.
Ororo's nephew starts exhibiting mutant powers, but he's more interested in settling a rivalry with a fellow mutant than hearing about a ""school for freaks"".
Kurt accidently finds an abandoned lab, and is sucked into a pocket dimension by a strange device he finds there.
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...
As an extra credit project, Evan is given a camera to record the ""current events"" in his life. Though most of them aren't keen on being caught on tape, Sabertooth is most definitively interested in the result.
While the X-Men are at a summer camp, learning survival training, Mystique releases Cain Marko - the unstoppable Juggernaut - in hopes of getting his help in obtaining Xavier's mutant location system.
Rogue's nightmares seem to show images from Kurt's past, but in them he's far too young to remember. So where did they come from?
A news report from the Canadian mountains triggers something deep inside Wolverine, and he starts having berserk fits. To find out why, he takes the Blackbird to the site, not knowing that Kitty and Kurt are sitting in the back.
As mysterious metal pods appear, picking up the mutants one at a time, Cerebro detects a new mutant in Hawaii: Alex Summers - Scott's believed to be deceased brother.
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.
When Scott and Kurt use their powers to save several people from a car crash, the question of how much they're willing to ignore to keep their powers a secret comes up. Professor X maintains that the world is not ready to know about them, however the other mutants, now without Mystique's guidance, have other ideas...
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.
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""...
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.
The kids get worried when the normally cool and collected teacher Hank McCoy starts having fits of animal rage.
Scott becomes lost at sea when trying to find his brother, who was swept out by a freak wave while surfing.
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.
An African witch-doctor comes to the institute to steal Storm's powers while she is faced with the decision to send Evan back to his parents.
Lance comes to the mansion, wanting to join the X-Men. Unfortunately he has a hard time fitting in, and it doesn't get any easier when he gets the blame for some of the other students' nightly joyrides in the various X-Men vehicles.
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.
Magneto steals the remaints of the top secret "Rebirth" project, a project Wolverine helped shut down all the way back in World War II.
Jean has nightmares about huge circus clowns, then is controlled by the master of that circus, with Nightcrawler, Kitty, and Spyke controlled also.
Forge is working on a device that will enhance Kurt's teleportation powers.
While Beast is taking Kitty, Bobby, Evan, and two other new recruits on a camping trip, a few hunters decide that Beast is really a Big Foot, and they plan to trap him.
Mystique breaks a mysterious young girl out of an asylum and brings her to the Brotherhood House.
Wolverine suddenly vanishes, as the Brotherhood members team up with the X-Men to defeat Magneto.
The Brotherhood and X-Men arrive where Magneto is with his new allies.
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.
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.
During the rebuilding of the manor, Kitty and Kurt intercept a bunch of graffiti artists disguised as monsters. The older students get to go back to Bayville High for one day before attending a hearing to determine their ultimate fate, while they are banned from using their powers.
Wanda goes searching for Pietro. Meanwhile the brotherhood's members are expelled from school, much to Lance's dismay.
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.
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.
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.
Rogue appears to have problems with her powers, as the residual impressions of everyone she has touched start flashing through her mind and body.
Mesmero mentally controls Gambit into stealing half of the Spider Stone from Angel.
The X-Men are on vacation with Storm as their guardian. Amara falls ill while on the ship.
A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by the Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.
As Jean's and Scott's graduation day approaches, Rogue suddenly leaves the mansion.
As all the monsters in the tomb attack, the teammates fight to survive and find a way out.
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.
When the Brotherhood saves a few people after Wanda accidentally causes a subway accident, they are regarded as heroes. The X-Men are utterly repulsed. The Brotherhood begins to cause accidents just to get famous. When the X-Men figure it out, Pietro tricks Wanda into using her powers to make it look like the X-Men are the villains. After the X-Men are arrested, the Brotherhood tries to cause one last accident. When they can't stop it, the X-Men are released to help. Shadowcat & Jean can't stop the explosion, so Avalanche does. He promises that there will be no more heroics.
Wolverine is kidnapped, but escapes in the forest. X23 returns and teams up with Wolverine to take on Hydra!
David Haller, Xavier's son, who has lived away from his father's knowledge, contacts him seeking help. He has been kidnapped by a man called Lucas. Xavier, Jean, Scott and Storm travel to Scotland where Xavier's ex-wife lives with David and a street boy called Ian. When Ian leaves the house, Jean follows him and is kidnapped by Lucas. Scott tracks them to an old castle in ruins where teenagers throw parties and gets captured. Xavier and David's mother find Ian and with his help, they get to the castle and face the boys there while Jean, Scott and David escape. David meets his father for the first time, and he reveals he is actually Ian. Lucas, too, by turning into Ian first and later into Lucas. His multiple personalities change his appearence every time. Xavier enters in his son's mind trying to erase Ian and Lucas, but fails and Lucas is the only one left who disappears in the sky. Meanwhile, at Bayville, Kitty and Kurt are way too sick to go to school.
A further mutated Spyke, now armored and able to throw flaming spikes, now protects mutants, including Magma and Cannonball who are walking out of a library when Duncan pulls up and tries to attack them. Xavier is concerned and sends a reluctant Wolverine to talk to him, to no effect. Callisto is also concerned that Spyke's efforts will bring down the wrath of mutant-haters on the other Morlocks who can't protect themselves. Her predictions come true when Spyke's efforts set off further anti-mutant hysteria. Spyke protects a young mutant named Dorian Leach, who it is revealed to have the power to suppress energy - electrical, mutant, whatever. The Morlocks and the X-Men come to Spyke's aid, and defeat Duncan and his men. Dorian shows up and temporarily negates everyone's powers. Duncan is arrested and Spyke returns to the underground. Meanwhile, Apocalypse creates a second sphere in China which resist all efforts to destroy it, and Nick Fury is ordered to free Trask and have him reinit
Gambit kidnaps Rogue and tells her he is trying to help her to forget what she did to Mystique. When everyone notice she is missing, Wolverine sense Gambit's smell and goes to Magneto's base where he find Pyro and tells him the Acolytes are separated and he does not know where Gambit is. Gambit takes Rogue to city where a couple of criminals reconcile him and attack them both. Rogue touches the leader of them and discovers Gambit's foster father is being hold in an old house near the swamp. They go there and Rogue accidentally touches Gambit and learns he is using her to get there. Gambit decided to go alone but Rogue comes back to help him and rescue his father and take on the Rippers. Wolverine and the rest of the X-men arrive and take Rogue with them while Gambit decides to quit that lifestyle for good.
Kitty is saved from a rockslide by a mutant girl named Danielle Moonstar. Danielle quickly joins the institute, but immediately causes trouble during a training session when she causes the nightmares of Jean, Kurt, and Kitty to come true. That night, Logan, Professor X, and Storm also have powerful nightmares, worrying Kitty that her new friend will be expelled from the institute. When Kitty wakes up the next morning, Danielle isn't there -- and when she asks, nobody has even heard of her. Kitty is determined to find Danielle Moonstar, and follows a path of strange messages that only she is receiving to her location.
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 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.
