| ShortSummary | - The transformation of The Dark Phoenix is complete and she begins her rampage. When the X-Men confront the Phoenix and ask it to give up Jean's body, Dark Phoenix vows to destroy the team, defeating them easily. This forces The X-Men to try to figure out a way to expel The Phoenix Force from Jean's body without hurting her.
- Weary of battling for mutant supremacy, Magneto offers to transport all mutants to an orbiting asteroid named Asteroid M where they can live peaceful and human-free lives; however, Fabian Cortez tricks Magneto into an escape pod and launches him into space.
- When Cyclops flies solo to a tiny, western, desert community to see an old friend, his plane is blasted out of the sky. Injured and unable to use his powers, he struggles into town, only to discover his friend is missing and the town is caught in the grips of a militant, mutant-only, anti-human hate group: the Children of the Shadow.
- The X-Men are attacked by the Phalanx, a race of techno-organic aliens seeking to assimilate all life on earth. The alien Warlock allies with Beast, Forge, and Mr. Sinister to defeat the Phalanx.
- Mister Sinister uses a brainwashed Morph to lay traps to destroy the X-Men one by one.
- The alien Arkon comes to Earth and begs Storm to return with him to his planet, to save it from meteorological chaos which threatens his people. After much pleading, Storm agrees, but leaves a clue for the other X-Men to follow. Once successful, Storm is proclaimed savior throughout this universe. Then Arkon asks her to marry him.
- Archangel has become obsessed with destroying Apocalypse, who he blames for ruining his life.
- 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.
- The X-Men are attacked by the Phalanx, a race of techno-organic aliens seeking to assimilate all life on earth. Warlock, Beast, Forge and Mr. Sinister are trying to find help but Magneto at first sees this as his chance to watch humanity go down until he learns his son Quicksilver has been captured by the Phalanx.
- The X-Men and Magneto team up to stop Master Mold from replacing Senator Kelly's brain with a computer, and engage in an all-out battle against a score of Sentinels. Kelly calls off his anti-mutant campaign and Beast is freed from prison.
- 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.
- Longshot, rebel from another world, tumbles into this world with no memory. He's Disscovered by Jublile who takes a linking towards him and they both find themselves on the run from Mojo and his hunters.
- Garokk fuses with the island's volcano and the surging planetary force below it.
- Cable comes to the present to stop Bishop and save his own future world.
- 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.
- In London, England's Victorian era, two scientists, Dr. James Xavier and Dr. Nathaniel Essex, hotly debate Charles Darwin's theory of natural selection. Essex believes mutants are the next genetic step forward and begins a bizarre experiment involving mutant evolution. The origin of Mr. Sinister is revealed, as Dr. Xavier attempts to stop Essex before he goes too far.
- Jubilee leads a group of school children on tour of a cave on Mansion property, only to be caught in a cave-in. As the water in the cave rises, she keeps the kids calm by spinning a medieval fairy tale of knights, princesses, trolls and dragons. Some of these characters might just seem to resemble the X-Men. As she tells the kids the stories, the real X-Men arrive and save them.
- An alien, Mojo, kidnaps and casts the X-Men as his latest all-galaxy television hit.
- After destroying the files on mutants, the X-Men escape to the Blackbird, but are stopped by the Sentinels. During the fight with the Sentinels, Morph is killed and Beast is captured and imprisoned by the government.
- 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.
- Omega Red, the destruction machine from the former Soviet Union and a sworn enemy of Wolverine, is thawed and sent two miles beneath the ocean to salvage a disabled, toxic nuclear submarine threatening to break up near Hawaii. His only condition: Wolverine and Storm go down with him as insurance.
- Apocalypse turns mutants who journeyed to Muir Island seeking the fictitious cure into the Horsemen. Apocalypse and his four Horsemen attack the World Peace conference in Paris. Rogue absorbs Archangel's dark side.
- Juggernaut's life is at risk when someone else uncovers the Ruby of Cyttorak and claims the powers of Juggernaut for himself.
- Gambit is forced to return to his southern roots by an ancient tithe, an old family feud and the kidnapping of his brother, Bobby.
- The X-Men and Banshee go to save Lilandra from Juggernaut and Black Tom Cassidy Lilandra reveals that she arrived on earth seeking help in protecting The M'Kraan Crystal from her tyrannical brother D'Ken. Jean Grey continues to exhibit inexplicable symptoms and fully embraces The Phoenix persona to come to the rescue of the X-men from Sh'iar Imperial Guard Gladiator.
- It's the final episode for the X-Men. At a Mutant/Human Relations Summit, Henry Peter Gyrich attacks and cripples Professor Xavier with an energy disruptor. The X-Men and Moira MacTaggert try to save Xavier, but all seems lost. Lilandra comes and has a cure, but Professor Xavier must leave and go with her to the Shi'ar Empire to be cured. Meanwhile, Magneto makes final preparations to take over the world with his mutant army, but on the eve of the invasion Cyclops, Wolverine, and Jean Grey infiltrate Genosha to tell Magneto that Xavier is dying. He halts the assault on humankind out of respect for his greatest enemy, equal, and only friend. The final scene of the show depicts a lasting moment as all of the X-Men and Magneto stand outside the X-Mansion and say goodbye to Xavier as he leaves with Lilandra and her ship to the Shi'Ar home world.
- Wolverine's former sweetheart and girlfriend, a pretty Japanese woman named Yuriko, hesitantly lures Wolverine into the Morlocks' tunnels with Gambit and Jubilee tailing behind Wolverine.
- An emissary of the alien race the Shi'ar, Erik the Red takes over the Eagle One space station. Compelled by mysterious visions, Professor Xavier send the X-Men to take the places of the astronaut crew which leads to a confrontation with Erik and his mind controlled Astronauts. While entering the Earth's Atmosphere on a space shuttle, Jean Grey gets possessed by The Phoenix Force.
- Wolverine encounters Sabertooth in the Arctic, while Storm, Gambit, and Jubilee head to the "mutant loving" island paradise of Genosha.
- 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.
- Xavier and Magneto are the bait as Mister Sinister lures the other X-Men to his fortress in the Savage Land.
- The Phoenix continues to inhabit Jean's body. Jean is beginning to lose control, and the Phoenix begins to brazenly take over at will. When the Inner Circle Club learn of the Phoenix's power, they use Jason Wyngarde to create a new history in the mind of the confused Jean/Phoenix. While protecting Dazzler, a mutant club singer from being abducted by the Inner Circle, Cyclops and the X-Men get caught in this dangerous affair.
- 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.
- Mister Sinister and his Nasty Boys kidnap Cyclops and Jean Grey, while the X-Men battle Morph at the mansion.
- When the X-Mansion is trashed, the X-Men initially blame the Russian mutant Colossus, before discovering the real culprit is the Juggernaut.
- Cyclops discovers that Corsair may be his father. Corsair is on the run from Shi'ar authorities, who demand that Cyclops turn him over to them.
- 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.
- In the Shi'ar court, Lilandra reveals Phoenix's destruction of the D'Bari solar system and declared that Phoenix has transformed into the Destroyer of legend and must die. Professor Xavier calls for a Trial of Combat for the custody of Jean Grey/Dark Phoenix which pits The X-Men to battle The Shi'air Imperial Guard on The Blue Area of the Moon as both the fate of Jean's soul and the universe itself hangs in the balance.
- Mystique, Rogue's foster mother, forces her to revisit her own past.
- The space shuttle crash-lands in Jamaica Bay. Though the other X-Men are unscathed, Jean Grey's fate is unknown, until she flies into the air, displaying powers and a new costume she has never used before, and proclaims herself "The Phoenix" before collapsing, suffering from confusion, memory loss, and vast new powers. Meanwhile, Professor Xavier's pained psychic connection with an alien presence manifests in an Astral projection of Xavier's dark side whose hell-bent on destroying The X-Men.
- Cyclops and Jean are captured by a group of human mutants called the Morlocks when they go out on a romantic date, much to Logan's hurt. Storm battles their leader Callisto for control of the underground mutant group.
- Sam Guthrie's parents have contacted Professor Xavier about their son's mutant powers. Rogue goes back to the South to check things out and finds Sam living the life she never had. Family and friends support the young Cannonball, but Rogue must teach him how the rest of the world lives when shadowy Army officials attempt to use the youthful mutant.
- Cyclops, still in mourning after Phoenix's death, quits the X-Men and returns to the orphanage he grew up in and encounters his friend Sarah. Cyclops suspects foul play of Zebediah Killgrave, Sarah's wealthy benefactor as he begins to adopt mutant children for an unknown purpose.
- Nightcrawler gets a mysterious message. He is informed that his birth mother 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.
- 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.
- D'Ken gets pulled into the Crystal, and becomes one with the universe inside it. This forces both The X-Men and The Imperial Guard to team up to desperately combat the seemingly omnipotent dictator to no avail as the Earth is suffering a multitude of environmental disasters thanks for the unstable M'Krann Ckyrstal. Can the return of Phoenix help turn the tide?
- Spectacular preparations for Storm's wedding to Arkon proceed quickly. Meanwhile the X-Men discover that Arkon is a ruthless tyrant.
- Beast falls in love with Carly, a blind patient of his. Carly's father is a rampant mutant hater until the Friends of Humanity thugs kidnap Carly.
- The X-Men discover the truth behind Genosha as Gambit, Storm, Jubilee and a host of other mutants are made to work as slaves in order to complete a dam which will power a Sentinel factory. Meanwhile Gambit meets the mysterious Cable.
NOTE: As episode #8 wasn't finished in time, the first broadcast ending did not feature the X-Mansion wrecked.
- Phoenix transports most of the X-Men to Lilandra's ship , where she has hidden the M'Kraan Crystal. A group of space pirates called the Starjammers attack and steal the M'Kraan Crystal from the X-Men. The Starjammer's Leader Corsair plots to use The Crystal as bait to assassinate D'Ken and convinces Cyclops to aid him in his plan which goes terribly awry.
- The day Morph rejoins the X-Men, terrorists attack a top-secret, high-tech weapons factory; the alert interrupts his homecoming party.
- Sauron kidnaps Storm to the Savage Land in order to feed from her mutant energy.
- Yuriko's alien discovery — a Shi'ar vessel — turns out to be a prison cell containing a voracious, gaseous prisoner, the Spirit Drinker.
- As Magneto plummets helplessly to Earth, Fabian Cortez assumes control of Asteroid M and sends hundreds of missiles towards Earth. Meanwhile, Rogue goes to help the X-Men and tries to find a missing Gambit. Magneto frees himself and returns in time to destroy both the missiles and Asteroid M. Everyone escapes before the asteroid is destroyed and they all return home Meanwhile, Cortez is rescued from the descending asteroid by Deathbird... and Apocalypse!
- Wolverine witnesses the crash of a spaceship carrying horrific, alien bug-like creatures—the Colony—which overwhelm him. Meanwhile, Rogue has a run with Cody who offers her a chance to be together again but at the cost of her humanity.
- The X-Men come to the aid of Jubilee when her foster parents turn her in to the Mutant Control Agency and she is attacked by Sentinels. The X-Men discover that the group running the Mutant Registration Program intends to track and eliminate mutants.
- Bishop and the X-Men go to Washington and stop the assassination of Senator Kelly, but Bishop returns to find the future unchanged.
- Professor X tries to heal Sabertooth against Wolverine's warnings, while Magneto attacks a chemical plant in order to attract the attention of Professor X.
- 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.
- Omega Red is resuscitated by three corrupt generals who want to reclaim and rule the crumbling old Soviet empire. Colossus goes to the X-Men for help to save his country and its fragile freedom from these forces of tyranny.
- Wolverine thinks back to the time when he fought during World War II and teamed up with Captain America. Wolverine and Captain America must break into a Nazi establishment to rescue a kidnapped scientist, and fight the Red Skull.
- In a future controlled by Sentinels, Bishop is sent back in time to stop a member of the X-Men from assassinating an important political figure.
NOTE: The Punisher shows up on a video-game cartridge and Jean makes a reference to her "dark" past.
Tombstones appear for Cyclops , Rogue , Storm , and Jubilee .
- Fabian Cortez kidnaps Jubilee because Apocalypse is trapped in the Astral Plane and needs a host body. Cortez brings her to a temple, but Beast comes and rescues Jubilee and destroys the temple. At the end, when Apocalypse comes out of a portal, he takes over Cortez's body, transforming it into his form and banishing Cortez from it.
- Cable uses his time device and sees that Bishop traveled from 2055 AD to the present to stop a plague, which Apocalypse started.
- 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.
- When Professor X suffers a slight concussion, his powerful psychic mind is suddenly open to manipulation. The Shadow King takes advantage of this and takes possession of Xavier, leaving his mind trapped on the Astral Plane.
- Former X-Man Bobby 'Iceman' Drake is caught breaking into a top-secret government installation.
- 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.
- Rogue goes to Muir Island for an experimental treatment to rid her mutant powers and narrowly escapes becoming the slave of Apocalypse.
- Magneto attempts to break Beast out of prison, but Beast would rather stand trial. Sabretooth demands that Beast be set free and ends up going into a destructive rage, prompting the guards to shoot and injure him. Cyclops aids Sabretooth and brings him to the Mansions' infirmary, which does not sit well with Wolverine. Later, Magneto attacks a military missile facility.
- 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.
- Vindicator and Alpha Flight capture Wolverine. They demand to know the secret of his Adamantium skeleton.
- As Professor X and Emma Frost battle for psychic control of Jean, the Inner Circle members quarrel over how to dispose of their prisoners, the X-Men. Meanwhile, The Phoenix begins to grow in her thirst for new evil sensations and turns on both The Inner Circle and The X-Men.
- Gambit, Rogue, and Wolverine take a ski trip in Germany. While Gambit and Rogue seem to be largely enjoying each other's company and time together, 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.
- The Shadow King lures Storm home to Mt. Kilimanjaro by 'possessing' her young spiritual son Mjnari, so Rogue and Storm travel to Africa to stop the Shadow King.
- Upon touchdown in the Savage Land, the X-Men's mutant powers have been neutralized by Sinister's machines and they are immediately captured by the Nasty Boys and Mutates.
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