"The Cauldron" Part Two: 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.

"Strategy X": 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.

"The X-Impulse": 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!

"Grim Reminder": 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.

"The Cauldron" Part One: 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.

"Day Of Reckoning" Part Two: The X-Men are shocked when Professor X teams them up with the Brotherhood to stop them, but then, a shocking twist reveals that nothing was to be as it seemed to be.

"Shadow Dance": The Bayville High Sadie Hawkins dance arrives, and everybody is scrambling for dates. Jean is highly jealous of Scott's date. In the meanwhile, Forge constructs a device which augments Nightcrawler's teleportation, but is unaware that vicious monsters from Kurt's bamf dimension will now be able to enter Earth.

"African Storm": Storm is tormented by Houngan, an evil African shaman who wants to take over Africa. Storm and the X-Men have to stop an enemy who knows every weakness of hers.

"Walk On The Wild Side": The female X-Men are fed up with playing second fiddle, and form a vigilante crime-fighting group. For a while, things go great, but in the end, an old enemy crosses their way.

"Mindbender": A mysterious hypnotist named Mesmero kidnaps some of the X-Men and brainwashes them into committing crimes for him.

"Dark Horizon" Part One: 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.

"Dark Horizon" Part Two: 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.

"Impact": 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.

"Cruise Control": Looking to relax a bit, the X-Men go on a vacation cruise, but find that their fellow vacationers resent their mutant abilities. Seeking refuge from the hatred, several students go to a nearby island where the situation soon turns deadly as the island's volcano begins to erupt. Meanwhile, Magma falls unexplainably ill. When she reaches the island she seems to be the source of the volcanic eruption. Mighty she also hold the solution?

"Ghost of A Chance": 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.

"Ascension" Part One: 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.

"Ascension" Part Two: 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.

"No Good Deed": 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!

"Target X": 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.

"Sins of the Son": 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.

"Uprising": 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.

"Cajun Spice": 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.

"Self-Possessed": 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.