"X-23": 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.

Magneto destroys a chemical plant to draw the X-Men away from their headquarters. While the X-Men are away, Sabretooth breaks away from his wrist bindings and captures Jubilee. But when Wolverine discovers his nemesis holding Jubilee captive, things escalate to a feverish pitch.

"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.

Wolverine flees to Canada to seek solitude in the Canadian wilderness. He finds peace among a group of Baffin Island Inuit, only to discover Sabretooth has been stalking him and has taken the people of the village captive, and plans to kill them all.

"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?

"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.

When Professor X sends a mission to destroy the mutant registration files, things go terribly wrong and the X-Men must cope with the heavy price of fighting for mutant equality.

"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.

"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!

"Night Of The Sentinels" Part 1 After being attacked by a group of robots known as the Sentinels, Jubilation Lee meets the X-Men, a group of super heroes aiming for peace between mutants and the rest of society.

"The Toad, The Witch, & The Wardrobe": 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.

"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.

"X-Treme Measures": 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.

"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.

"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.

"Day Of Recovery": The remaining X-Men and Brotherhood members go to Area 51 to save their captive members. However, when Cyclops traps the treacherous Mystique in Area 51 to blackmail her into saying where Professor X is, the squads split. The X-Men are now alone in a world which shuns them.

"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.