In the final stand against Apocalypse and his horsemen, the X-Men, Brotherhood, and Acolytes all work together to take their common nemesis down before Apocalypse can wipe out humankind and turn them into mutants.
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Professor Xavier locates Apocalypse in Egypt and upon confronting him, disappears. While Apocalypse unleashes his four horsemen, the X-Men split into four different teams to defeat the deadly foes. To aide the fight, S.H.I.E.L.D. sends in Sentinels to attack the Apocalypse.
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A young mutant named Danielle Moonstar saves Kitty from danger and Kitty gets her to join the Institute. Soon Danielle’s presence at the school causes the other students to have powerful nightmares. When Danielle disappears, nobody at the school seems to remember her except for Kitty, who still receives messages from the strange girl.
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Gambit kidnaps Rogue, telling her he’s there to help her forget her troubles. But little does she know that Gambit has ulterior motives. When the X-Men realize Rogue is missing, Wolverine smells Gambit’s scent and the team sets out after her. Meanwhile, Gambit uses Rogue to help him rescue his foster father.
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When hate-crimes against mutants wreak havoc through Bayville, Spyke returns, having mutated further, to put an end to the violence. With the help of the Morlocks and the X-Men, the clan do their best to stop the anti-mutant sentiment before it gets out of hand. Meanwhile, Professor Xavier and Beast investigate Apocalypse’s activities.
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Professor Xavier is called off to Scotland when he learns that he has a son—who has been kidnapped! With the X-Men in tow, Professor Xavier arrives in Scotland only to learn that his son is not who he says he is.
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After being kidnapped on an airplane by Omega Red, Wolverine manages to escape to a nearby forest. There he finds his clone, X-23, on a mission to destroy the person responsible for creating her, Madame Hydra. Now the two team up to take on HYDRA and destroy the HYDRA base.
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When the Scarlet Witch accidentally causes an accident in the subway, the Brotherhood saves some of the innocent bystanders, making them look like heroes. Enjoying their heroic fame, the Brotherhood continues creating accidents only to pick up the pieces afterwards. When the X-Men discover their scheme, they confront the Brotherhood but the unknowing witnesses confuse the X-Men as the villains!
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While the X-Men try to learn more about Apocalypse in order to overcome him, Magneto sets out to tackle the being directly. When the crew finds Apocalypse somewhere in Mexico, they go to confront him before Magneto does anything drastic. Also, the X-Men decide what do to about Mystique who was turned into stone during their last battle with Apocalypse.
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On vacation, the X-Men go on a cruise but find that their fellow vacationers resent their mutant abilities. Seeking refuge from the hatred, several students go to a nearby island. The situation turns deadly when the island’s volcano begins to erupt.
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With Rogue under his control, Mesmero manages to use her to release Apocalypse from his tomb. When the X-Men, Brotherhood, and Acolytes make it to the tomb, strange monsters confront them. With the X-Men distracted, Mesmero, using both Rogue and Mystique, manages to release Apocalypse. Before the X-Men can fight Apocalypse, he absorbs all of Rogue’s powers and escapes.
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Mesmero attempts yet again to free Apocalypse, this time with Rogue as his pawn—using her to steal the abilities of the X-Men, Brotherhood and Magneto’s Acolytes. While the X-Men team up with Magneto and the Acolytes to thwart Mesmero, Wolverine, Sabretooth and Gambit set out to find Rogue.
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Wolverine discovers that HYDRA scientists have used a DNA sample from his tissue to clone him and create a new Weapon X. When the clone (code-named X-23) escapes, it targets Logan and anything else in its path, especially the X-Men.
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The menace Mesmero returns again to free Apocalypse from his incarceration. This time, Mesmero uses his mental powers to control Gambit, using him to acquire the means necessary to release Apocalypse. When Angel intercepts Gambit, he goes to the X-Men and enlists their help.
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Rogue starts having trouble controlling her powers when all the abilities she’s absorbed over the years begin to surface again. When she inadvertently absorbs Mystique’s shape shifting abilities, Rogue begins to morph into the many mutants whose powers she’s acquired, including the vicious Sabretooth. Now the X-Men have to defeat one of their own before Rogue does too much damage.
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While Wanda is in search of her father, Magneto, Toad steals Nightcrawler’s holo-image inducer in attempt to alter his appearance and woo the Scarlet Witch. When Wanda confronts Magneto, he uses the mutant known as Mastermind to erase Wanda’s memories of her troubled childhood.
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When the Morlocks create a new sports drink that’s harmful to mutants, it finds its way into Spyke’s hands at a Skateboarding Competition. To make matters worse, Spyke’s powers are becoming more and more uncontrollable and his temper is following suit. Meanwhile Kitty learns to drive, horrifying her worried fellow mutants.
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While the X-Men work to restore Xavier’s Institute after its devastating destruction, Mystique manages to break free of her incarceration. She soon sets a plan in motion that leads Cyclops into a deadly trap. Following his psychic signals, Jean and the Professor set off to rescue Cyclops from Mystique.
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When the Brotherhood is expelled from school with nowhere else to go, Magneto sends Gambit to get them to join his side. Meanwhile, Wanda gets her brother Pietro arrested and Magneto sends Gambit and his new recruits to break his son out of jail.
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Now that the world knows about mutants, Professor Xavier urges the X-Men and the Brotherhood’s return to school to convince their peers they pose no threat. However, the school’s Principal Kelly has other plans for the student mutant population.
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With Professor Xavier and Wolverine missing in action, Cyclops leads the X-Men to go find them while Storm and Beast battle the unstoppable Juggernaut. Also, they confront the government concerning the public knowledge of mutants.
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After the devastating cliffhanger ending of Season 2, the X-Men and the Brotherhood must pick up the pieces following the destruction of the X-Mansion. Discovering that Mystique, posing as Professor Xavier, was responsible for the explosion, the remaining X-Men set out to find their captured comrades and the real Professor.
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While chasing Sabretooth, Wolverine is attacked and captured by a group of anti-mutant commandos who want to us him as a test subject for the new Sentinel project. Meanwhile, in an effort to finally defeat magneto, Professor Xavier arranges a team up between the Brotherhood and the X-Men. After the X-Men go after Magneto, Xavier’s institute starts to self-destruct. As the countdown begins, several students are trapped within the mansion!
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The X-Men, along with their new teammates the Brotherhood, engage Magneto, but not before they learn about a traitor in their midst! While the battle rages on, Magneto caves in the ground unleashing the deadly Sentinel robot. The few mutants who manage to make it away from the Sentinel retreat back to the mansion only to discover that it’s been destroyed! Who could be responsible?
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In an effort to strengthen the Brotherhood once and for all, Mystique frees the mutant known as Scarlet Witch out of an asylum. Little does Mystique know that Scarlet Witch has a score to settle with her brother Quicksilver and her father Magneto.
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Hoping to reverse the effects of aging, Magneto steals the remaining components of a classified project entitled "Rebirth," the same project responsible for Captain America. Thinking he shut down the project for good during World War II, Wolverine now must finish what he started so many years ago, before it’s too late.
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When some of the male students antagonize Jean and Amara for having weaker powers, with the help of Tabitha, the girls decide to form a crime-fighting team. Soon joined by Kitty and Rogue, the group of girls, calling themselves the Bayville Sirens, takes to the streets at night to fight crime.
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While out on a camping trip with Kitty, Bobby, Evan, and some new students, a group of hunters mistake Beast for Big Foot. Now with the help of the accompanying mutants Beast must avoid being the hunters’ ultimate prize.
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Forge invents a device that allows Nightcrawler to teleport over much larger distances. Little do they know that now when Nightcrawler teleports he passes through a strange dimension. After each teleportation, he leaves a small portal from the dimension open. When strange beasts follow Nightcrawler out of one of the portals, they wreak havoc on the school.
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When a telepathic mutant named Mesmero possesses Jean, he uses her to gain control of the other students. With Jean, Nightcrawler, Kitty, and Spyke under his control, Mesmero attempts to steal ancient keys to release the imprisoned Apocalypse, an all-powerful mutant bent on enslaving the human race.
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When reports of a mysterious “guardian angel” flying around New York saving people in distress flood the media, Xavier believes the man to be a mutant. But with most of the X-Men away for Christmas and Cerebro out of commission, the Professor sends Cyclops and Rogue to track the strange angel character down before Magneto can get to him.
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Avalanche arrives at Professor Xavier’s Institute asking to be a part of the X-Men. Having enough trouble fitting in with the other students because he used to be in the Brotherhood, matters worsen for Avalanche when he gets blamed for some of the other students’ joyride in the X-vehicles at night.
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Storm’s mutant abilities are soon in jeopardy when an African witch doctor arrives at the Institute and attempts to usurp her weather-altering powers to achieve god-like status. Now the X-Men must come to Storm’s aide to keep her abilities intact.
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While in Hawaii, Havok gets swept out to sea in a surfing accident. Scott attempts to rescue his brother, but gets stranded as well. He and his brother must work together in order to survive.
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After years of keeping his mutation under control with a special serum, Hank McCoy’s mutant powers become resistant to the serum that once kept him in check. Now his students become worried as McCoy begins to have animal-like outbursts as the beast within claws its way to the surface.
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A Juggernaut jailbreak pulls the grown-ups away from the X-Mansion, leaving the younger X-Men without adult supervision. Basking in their newfound freedom, the kids decide to throw a party. Catastrophe ensues when a few of the party guests find their way into Cerebro—nearly demolishing the mansion.
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When Jean begins to develop new telepathic abilities, they start coming in sudden surges that she can’t control. The abilities become harder to ignore when each surge of telepathy becomes increasingly harder to control. While the X-Men help Jean get a handle on her new powers, Hank McCoy joins the school’s faculty as the new science and gym teacher.
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A free-spirited new student named Tabitha arrives at the school and it doesn’t take long before Nightcrawler develops a crush. With a knack for disobeying rules, Tabitha finds herself grounded for her recklessness. When her scoundrel father shows up looking for Tabitha’s help in robbing a bank, things go even further south for the newcomer.
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Despite Professor Xavier’s urges to keep their mutant identities a secret, Cyclops and Nightcrawler question his advice after using their powers to save several people from a car crash. While Professor Xavier explains that society isn’t ready to know about mutantkind, Mystique and the Brotherhood have other plans – they terrorize a stadium full of people.
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After an epic battle against the Brotherhood, the X-Men are transported to Magneto’s base on Asteroid M. Here Magneto’s evil plans for the future of mutant kind are set in motion. Now Scott must convince his brother and help stop Magneto before it’s too late.
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Under the impression that Cyclops’ brother died 10 years ago, using Cerebro, Professor Xavier and Cyclops discover that Alex Summers, Havok, is in fact alive and well. In a race to get to Havok before Magneto can draft him, Wolverine and the X-Men are pitted against Sabretooth and the Brotherhood.
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When a strange news broadcast from the Canadian Rockies triggers a computer chip in Wolverine’s brain, he begins to have unusual fits of rage. Lured to Canada and the lab where he got his adamantium skeleton and claws, he falls straight into one of Sabretooth’s traps. Fortunately for Wolverine, Kitty and Kurt stowed away in the Blackbird and are on the scene to provide some much needed back up.
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When Rogue begins having strange nightmares about Nightcrawler’s past, she becomes curious of their origin. As the dreams intensify, Rogue and Nightcrawler set off to learn the true secrets of who Kurt is and who his mother is!
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Away from the institute, the X-Men are thrown in a survival training boot camp with the Brotherhood. While the young mutants are out of the picture, Mystique frees Cain Marko, the unstoppable Juggernaut, from his imprisonment in hopes of gaining access to Xavier’s School. However, cooperation isn’t on Juggernaut’s mind when he takes off on a rampage of revenge against his half-brother.
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For a school project, Spyke gets a video camera to document life as a teenager. While Spyke videotapes his fellow X-Men, Sabretooth decides the video camera is the perfect way to find Wolverine and Xavier’s School along with it.
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While on a school geology field trip, Scott and Rogue realize that the schoolmates they thought they could trust have other plans. Now the two will have to work together in order to survive their rocky situation.
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When Rogue and Nightcrawler inadvertently stumble upon the abandoned lab of a mutant called Forge, Nightcrawler is accidentally sucked into another dimension by one of Forge’s inventions. Nightcrawler discovers that Forge himself has been trapped in the dimension since the 70s! It’ll take the help of the X-Men to get them back to the present!
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When Storm’s nephew, Spyke, begins to develop his mutant powers, he decides he’d rather use his unusual abilities for revenge against a thief calling himself Quicksilver, rather than learn to harness his powers at Xavier’s Institute.
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When hot-head Fred Dukes, The Blob, starts his first day of school, his girth and equally massive temper makes him one of the less popular guys in town. When Jean Grey tries to help him assimilate into his new surroundings, Blob mistakes her kindness for romance and tries to make her his girlfriend.
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After a young mutant named Rogue touches a fellow student and absorbs his energy and memories, she runs away from home, confused and frightened. Now it’s open to Professor Xavier and his students to recruit Rogue and help her before Mystique can turn her against the X-Men.
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When Kitty Pryde discovers her mutant ability to phase through objects, she’s naturally frightened and confused. Life proves to be more difficult for Kitty when both Jean Grey and Lance Alvers, a.k.a. Avalanche, approach her. While Jean tries to recruit Kitty to Professor Xavier’s Institute, Alvers has plans of his own. Meanwhile, Sabretooth, Wolverine's arch-nemesis, rolls into town and he’s looking for a fight!
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When high-schooler Todd Tolanski starts exhibiting toad-like mutant powers, Mystique sees a perfect opportunity to get a spy into Xavier's institute. Meanwhile the X-Men recruit a new member as Kurt Wagner joins Xavier’s school to learn to harness his mutant powers.
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