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...
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""...
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.
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.
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.
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.
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.
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.
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 hunts Apocalypse, but the X-Men hesitate. Kurt brings Mystique back from the Brotherhood, leading to a fight. Jean finds Apocalypse, and the X-Men investigate but fail to stop him. Apocalypse defeats Magneto. Rogue learns she can save her mother but shatters the statue, ignoring Kurt’s plea.
The Brotherhood stages accidents for fame, framing the X-Men. After their arrest, the X-Men help stop a final disaster, with Avalanche preventing the explosion and promising no more heroics.
Wolverine is kidnapped, but escapes in the forest. X23 returns and teams up with Wolverine to take on Hydra!
Xavier’s son, David, is kidnapped by Lucas, who has multiple personalities. Xavier and the X-Men rescue him, and David learns Ian is actually Lucas. Xavier fails to erase Lucas, who disappears. Meanwhile, Kitty and Kurt are too sick for school.
Spyke, now armored, protects mutants but sparks anti-mutant hysteria. He shields Dorian Leach, who can suppress powers, and the X-Men defeat Duncan. Dorian negates everyone’s abilities, and Duncan is arrested. Meanwhile, Apocalypse creates an indestructible sphere in China.
Gambit kidnaps Rogue to help her forget her past with Mystique. Wolverine tracks him to Magneto’s base, but Gambit takes Rogue to confront his foster father’s captors. Rogue discovers Gambit’s plan and helps rescue his father. The X-Men arrive, and Gambit decides to leave his old life behind.
Kitty is saved by Danielle Moonstar, a mutant who joins the institute but causes nightmares for Jean, Kurt, and Kitty during training. When Danielle disappears without a trace, Kitty follows mysterious messages to find her, fearing she might be expelled.
Professor X and Storm attempt to communicate with Apocalypse, but their efforts fail. Apocalypse sends out four horsemen to protect his spheres, and the X-Men split into teams to confront them.
The X-Men and Brotherhood struggle against the horsemen as Apocalypse’s plan escalates. With time running out, the teams fight desperately to stop him, but the outcome remains uncertain as they face unforeseen challenges.
