Part 1 of 3. In the series premiere of this animated take on the popular comic-book heroes, a solo-traveling Wolverine finds he's still angry a year after the Xavier Institute was destroyed. When a family he saves is punished for showing him kindness, he resolves to reunite the X-Men.
Part 2 of 3. Wolverine encounters obstacles when trying to get the team back together: Some members can't be found, and others refuse to join him. As for Rouge, she's already joined another group---the Brotherhood.
Conclusion. Emma Frost wants to be a part of the team, so she locates Professor X and uses this info to join the X-Men. Wolverine then organizes a dangerous rescue mission that involves facing Magneto.
Professor X tells Wolverine that he must prevent Africa from being destroyed by Storm, whose mind is possessed by the Shadow King.
Wolverine teams up with Gambit to recover a collar that can inhibit mutant powers.
Nightcrawler tries to help refugee mutants who are being mistreated by crews on cargo ships, but then he must also save them from an even worse danger: pirates.
Nick Fury blackmails Wolverine into taking down the Incredible Hulk, who's been on a rampage, but then Wolverine realizes that he must also fight Wendigo, who's loose in the wilderness as well.
The X-Men accept an unfavorable mission: save the Brotherhood and deliver Nitro to the MRD in exchange for saving half the world's mutants. However, Nitro's inability to control his powers causes unforeseen problems.
Future Xavier is captured by Sentinels who also take Cerebro, the mutant-tracking device. Xavier then teams up with fellow mutant prisoners to try to get Cerebro back.
Nightcrawler is initially happy to arrive in Genosha, but soon he learns the island is not the paradise it was made out to be. He then tries to evade Magneto's mutant assistants and warn the X-Men about the evils of the island.
Logan tries to get rid of his bad dreams by returning to the past.
A frantic Cyclops goes after Sinister, believing he is responsible for Jean Grey's disappearance.
The X-Men are preoccupied fending off an attack by the Brotherhood, which enables Magneto to begin a precision strike against nationwide MRD facilities.
Logan teams up with Mystique to infiltrate Weapon X and rescue a kidnapped woman whose father Logan abducted while he was a Weapon X agent.
A brainwashed Wolverine is brought in by Mojo to hunt down Nightcrawler.
Wolverive is captured while on a recon mission, and Bolivar Trask tries to get some information on his powers. Twenty years in the future, Wolverine-like Sentinels come after Professor X and his team.
Logan discovers the X-Men are kidnapped and knows that the Silver Samurai is behind it. He then tracks down the Silver Samurai in order to fight him.
The X-Men try to stop a future war between Xavier and Master Mold, but they walk into a setup and must fight a warehouse full of Sentinels.
At his father's request, Angel is hunted down for helping fellow mutants. Angel's father then has his son's damaged wings removed. This leads Angel to take up Sinister's offer of new mechanical wings, and he transforms into the vengeful Archangel.
Cyclops' obsession with Jean leads him to get distracted and then injured, but he's hesitant to let Emma wipe Jean from his memories, However, he does allow Emma to peek at his thoughts; this reveals something surprising he didn't know about Jean.
The X-Men sneak into a facility to collect data storage from Master Mold and are assisted by Rover, an old-model Sentinel. However, while gathering the data, they get trapped inside the facility.
Wolverine and Nightcrawler try to stop Gambit, a mutant spy hired by Sen. Kelly to steal Magneto's helmet. Gambit admits his thieving intentions, but claims he would rather take refuge in the mutant paradise.
Emma and Scott locate Jean, whose memory is gone, and Sinister sends Archangel to get her. Jean and Scott are then taken captive.
Part 1 of 3. Future Xavier is captured and shocked by what he sees. Meanwhile, Wolverine locks up Emma because he believes she is responsible for Jean's disappearance, and the team tries to stop the Sentinels from arriving at Genosha.
Part 2 of 3. The Sentinels make Future Xavier locate the world's remaining mutants. Meanwhile, many of the X-Men are unconscious after a battle, and Emma and the five Cuckoos trick Jean, but soon the Inner Circle begins to question Emma's loyalty.
Conclusion. Magneto and his Sentinels begin their attack on the city; Scott is shocked to learn that Emma was working with the Inner Circle; Scott and Jean try to stop the Phoenix; Wanda and Mystique decide to fight with the X-Men to try to stop Magneto.