Episode 1 - Out of the Past (1)

A group of cyborg mercenaries, led by a woman from Wolverine's past, seek his forced help in unlocking the secrets of a long buried alien spacecraft.

Episode 2 - Out of the Past (2)

An alien being called the Spirit Drinker drains the life-force of Jubilee and the Reavers, making strained allies of Wolverine and Lady Deathstrike.

Episode 3 - The Phoenix Saga: Sacrifice (1)

Following visions from recent dreams, Professor Xavier sends his X-Men on a mission to the Eagle One Space-Station, putting them in the middle of an interstellar conflict.

Episode 4 - The Phoenix Saga: The Dark Shroud (2)

The X-Men barely survive their return trip from space, Jean Grey discovering herself changed by the experience. Professor Xavier's dark half is given form, and proceeds to attack his students.

Episode 5 - The Phoenix Saga: Cry of the Banshee (3)

Professor Xavier's claims of the capture of his alien soulmate Lilandra by Juggernaut and Black Tom Cassidy are met with skepticism.

Episode 6 - The Phoenix Saga: The Starjammers (4)

Lilandra seeks to protect the M'Kraan Crystal from her wicked brother, the Emperor D'Ken. But the interstellar pirates known as the Starjammers capture it, and Cyclops, in an effort to enact their own revenge scheme on the emperor.

Episode 7 - The Phoenix Saga: Child of Light (5)

Shi'ar Emperor D'Ken's rise to power via the M'Kraan Crystal is causing a universal implosion. The X-Men, Imperial Guard, and Starjammers find themselves overpowered and unable to stop it. Jean Grey must unleash her destiny as the host of the Phoenix, even at a most personal cost.

Episode 8 - Savage Land, Strange Heart (1)

Mutant-draining, pterodactyl-man Sauron is persuaded into capturing Storm by Zaladane, the high priestess of Savage Land Sun God Garokk, unaware of her ulterior motives for unleashing the mutant's full potential.

Episode 9 - Savage Land, Strange Heart (2)

Storm's unfettered weather-fury continues setting the stage for the rise of Garokk. Even if Storm can be brought back under control, the Sun God's geothermal rejuvenation will spell an end to the Antarctic paradise known as the Savage Land.

Episode 10 - Obsession

Fueled on by his desire to seek vengeance against the immortal mutant that changed him into a weapon of evil, Archangel persaudes Rogue into helping him hunt down and destroy Apocalypse.

Episode 11 - The Dark Phoenix: Dazzled (1)

The flirtation between Cyclops and a mutant singer named Dazzler exacerbates the Phoenix-controlled side of Jean Grey, leaving her open for manipulation by a secret sect of mutants coveting her immense powers for their own evil designs.

Episode 12 - The Dark Phoenix: The Inner Circle (2)

The Circle Club makes the Phoenix-controlled Jean Grey their new Queen, but finds two factors opposing it: her mental bond with Cyclops, and the presumed-dead Wolverine stalking after them.

Episode 13 - The Dark Phoenix: The Dark Phoenix (3)

As the Dark Phoenix grows increasingly hostile, even destroying an entire star system, the X-Men struggle to figure out a way to stop her without harming their teammate Jean Grey.

Episode 14 - The Dark Phoenix: The Fate of the Phoenix (4)

The X-Men face the Shi'ar Imperial Guard in a trial by combat to spare the life of Jean Grey, though even they begin to question the safety of the universe as long as the Dark Phoenix remains alive inside her.

Episode 15 - Cold Comfort

A founding member of the X-Men, named Iceman, breaks into a government facility. He refuses to trust his former teammates about his reasons for doing so, but when Jubilee aids him in his quest, it leads to the team going up against another group of mutants, known as X-Factor.

Episode 16 - Orphan's End

Cyclops discovers that Corsair, the leader of the interstellar band of pirates known as the Starjammers, is his father. He's a fugitive on the run from the Shi'ar empire, and seeks his help in proving his innocence. But can the man who abandoned him as a child truly be trusted?

Episode 17 - The Juggernaut Returns

Professor Xavier's step-brother, and sworn enemy, the Juggernaut loses his powers to a bumbling archeologist. He must overcome the pain of their childhood together, and have the powers restored to him to save his life.

Episode 18 - Nightcrawler

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.

Episode 19 - Weapon X, Lies, and Video Tape

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.

Episode 20 - Episode 20

Episode 21 - Episode 21

Episode 22 - Episode 22

Episode 23 - Episode 23

Episode 24 - Episode 24

Episode 25 - Episode 25

Episode 26 - Weapon X, Lies, and Video Tape

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.

Episode 42 - Delete - No Episode 42 in Season 3