The Juggernaut Returns
Season 4, Episode 1 TV-Y7
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Juggernaut’s life is at risk when someone else uncovers the Ruby of Cyttorak and claims the powers of Juggernaut for himself, wanting to pick up girls. Cyclops and Wolverine find the new Juggernaut and intervene. He drops the Ruby and Wolverine and Cyclops escape with it. Professor X gives the Ruby back to his step-brother, restoring the original Juggernaut. He throws the Ruby into space and leaves the X-Men without a fight.
Nightcrawler
Season 4, Episode 2 TV-Y7
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Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit and Rogue seem to be enjoying themselves, Wolverine is restless, and longs for some action. When he hears reports of a demon hiding in a local monastery, his investigation reveals not a demon, but a mutant, Nightcrawler, whose devilish appearance is in stark contrast to his peaceful and deeply philosophical nature. Later the townsfolk attack and burn the monastery. The X-Men convince the townsfolk not to fear what they do not understand, Wolverine, too, learns something about the nature of faith.
Weapon X, Lies And Videotape
Season 4, Episode 3 TV-Y7
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A cryptic postcard unleashes a flood of maddening and painful memories in Wolverine that threaten to drive him insane. To keep his mind from being torn apart, Wolverine and Beast travel to the one location that may hold the answers to his hidden past: the ruins of the top-secret Weapon X lab where Wolverine's bones were laced with adamantium. There he encounters other former 'test subjects'—Sabretooth, Maverick and Silver Fox—who are suffering similar mental breakdowns. Later they find out that many of their memories were implanted, and their true memories are destroyed with the lab.
One Man's Worth Part 1
Season 4, Episode 4 TV-Y7
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Trevor Fitzroy and Bantam travel back in time to 1959 and kill Professor X as Master Mold ordered them. This creates an alternate present time-line, where a human-mutant war has destroyed everything. Bishop and Shard arrive in 'alternate present,' where humans battle violently against 'The Leader' Magneto, and his followers who include husband and wife Wolverine and Storm. Bishop and Shard recruit Wolverine and Storm to help stop Fitzroy, but they fail.
One Man's Worth Part 2
Season 4, Episode 5 TV-Y7
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Failing to stop the assassination of Xavier, Bishop, Shard, Storm and Wolverine travel forward to the future, a future changed so much that Forge's time travel machine has never been tested, and Forge has no idea who these four time travelers are. After they convince Forge, they go back a few minutes before Xavier died and save him. Everything reverts to normal.
Proteus Part 1
Season 4, Episode 6 TV-Y7
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Moira MacTaggert is trying to help her son Kevin (Proteus), but when he escapes from Muir Island she calls on the X-Men for help. Proteus who has never been off the island is wreaking havoc while trying to find his father.
Proteus Part 2
Season 4, Episode 7 TV-Y7
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When Proteus discovers that his deadbeat dad is a prominent politician, he storms the Union Hall right in the middle of his dad's campaign speech on 'family values.' Proteus tells his father that he is his son, his father denies it and runs off in horror, crying for help. Angered at his father's reaction, Proteus creates havoc, but Professor X later calms him down, and he stops the rampage. Then he goes back to Muir Island with Moira MacTaggert
Beyond Good & Evil (Part 1): The End of Time
Season 4, Episode 8 TV-Y7
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In 3999 Apocalypse tricks Cable and steals Cable's time device and goes back in time, but he accidentally falls in the axis of Time. Apocalypse hires Mister Sinister to kidnap psychics all across the universe. Meanwhile, Jean and Scott try to get married again
Beyond Good & Evil (Part 2): Promise of Apocalypse
Season 4, Episode 9 TV-Y7
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Apocalypse kidnaps Psylocke, Jean Grey and Professor X. Meanwhile Bishop also gets trapped in the axis of time. Also, Cable and his son break into a government base to steal a time-device.
Beyond Good & Evil (Part 3): Lazarus Chamber
Season 4, Episode 10 TV-Y7
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Cable also uses another time-machine and comes to the present to get the X-Men’s help in destroying Apocalypse's Lazarus Chamber. They go back in time to ancient Cairo and destroy the chamber. Apocalypse plans to use the psychics to destroy all time, and recreate a universe, where he will rule unchallenged
Beyond Good & Evil (part 4): End & The Beginning
Season 4, Episode 11 TV-Y7
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As the true and terrifying nature of Apocalypse's final plan emerges, several in his band team up with the X-Men to stop him. With Bishop's help the psychics are freed. At the end the psychics move Apocalypse to the Astral Plane, so he could age without the help of his chamber
Have Yourself a Morlock Little X-Mas
Season 4, Episode 12 TV-Y7
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As all of the X-Men prepare for a festive Christmas, foster child Jubilee is thrilled. She, Storm, and grouchy humbug Wolverine go last-minute shopping in Manhattan, only to be caught in a life-or-death crisis involving Leech, the littlest Morlock. Leech needs blood transfusion, so Wolverine's blood is given and then Leech gets better. Additionally Storm agrees to give back to Callisto her title as the Morlock's official leader
Lotus And Steel
Season 4, Episode 13 TV-Y7
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Wolverine, losing control, quits the X-Men and returns to the rural Japan of his younger days, in an effort to find himself. He works peacefully with a former spiritual teacher, the monk Oku, to build a temple. But the neighboring village is about to be attacked by bandits, led by the merciless Silver Samurai, unless payment is made. Some of the villagers want to resist, and ask Wolverine for help. Wolverine is torn. This is just the sort of thing he had wanted to leave behind. Wolverine bests the Samurai in single combat by taking advantage of Samurai's habit of teleporting in behind him: Wolverine anticipates the move and disables the teleportation device, humiliating Samurai.
Family Ties
Season 4, Episode 14 TV-Y7
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Shortly after Magneto breaks into the X-Mansion, High Evolutionary and his New Men capture him, Quicksilver, Beast, Wolverine and Scarlet Witch, to do experiments on them. He also reveals that Magneto is Quicksilver and Scarlet Witch's father. The other X-Men later defeat High Evolutionary and His New Men, and save the captured mutants. During this episode, High Evolutionary transformed Wolverine into a werewolf
Bloodlines
Season 4, Episode 15 TV-Y7
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Nightcrawler gets a mysterious message. He is informed that his birth mother (whom he never knew) is in trouble. He turns to the X-Men for assistance. Jubilee is baffled that Nightcrawler wants to help the mother who abandoned him. Nightcrawler admits there has been pain, but his faith in God has helped him overcome her rejection. The plot thickens when one of the team members recognizes Nightcrawler's mother's voice