Out of the Past Part 1
Season 3, Episode 1 TV-Y7
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Wolverine's former love, a Japanese woman named Yuriko, lures Wolverine into the Morlocks' tunnels with Gambit and Jubilee tailing behind Wolverine. She hopes to make a stunning alien discovery with Wolverine's help. They discover a ship, and Wolverine opens it.
Out of the Past Part 2
Season 3, Episode 2 TV-Y7
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Yuriko's alien discovery — a Shi'ar vessel — turns out to be a prison cell containing a voracious, gaseous prisoner, the Spirit Drinker (a possible reference to the id monster from the 1956 Sci-Fi classic, Forbidden Planet). It immediately sucks life out of Jubilee, Yuriko and her cohorts, the Reavers. After arriving with reinforcements, Professor X goes to the ship and learns more about what is going on while the rest of the team work towards preventing the Spirit Drinker from reaching the surface. Soon at the subway tunnel, Wolverine discovers that electricity makes the alien explode and Gambit throws his metal staff on the railroad track to serve as a conductor on harnessing electricity to defeat the alien.
Phoenix Saga Part 1: Sacrifice
Season 3, Episode 3 TV-Y7
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An emissary of the alien race the Shi'ar, Eric The Red takes over the Eagle One space station. Professor Xavier has been suffering from troubling visions and loss of control over his powers since the X-Men's encounter with the Spirit Drinker. Aware of something occurring in space, he sends the X-Men go to the space station to stop Erik the Red from killing the astronauts. While returning, they collide with an energy wave. Jean Grey, realizing she is the only one who stands a chance, knocks Cyclops out to prevent him from stopping her, absorbs the pilot's training telepathically and telekinetically pilots the shuttle while the others sit in a chamber that shields them from the radiation, sacrificing herself. When her shields begin to fail, she cries for help and the Phoenix Force answers her psychic call.
Phoenix Saga Part 2: The Dark Shroud
Season 3, Episode 4 TV-Y7
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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, Xavier goes to Muir Island to recuperate after his mind is attacked and a psychic projection of his dark side attacks the X-Men; an alien named Lilandra Neramani has come to seek Xavier's help, but Juggernaut and Black Tom Cassidy kidnap her.
Phoenix Saga Part 3: Cry of the Banshee
Season 3, Episode 5 TV-Y7
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The X-Men and Banshee go to save Lilandra. Jean Grey continues to exhibit inexplicable symptoms. Lilandra explains that her brother, the Emperor of the Shi'ar, has gone insane and power-hungry, and seeks to control the M'Kraan Crystal, an object whose power threatens to destroy every universe in existence. Here they are met by Gladiator, the leader of D'Ken's guard, and cannot defeat him. Jean transforms fully into Phoenix and easily defeats Gladiator before declaring herself the Child of Light, Guardian of the M'Kraan Crystal and of creation.
Phoenix Saga Part 4: The Starjammers
Season 3, Episode 6 TV-Y7
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Phoenix transports all 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. Phoenix reads the leader, Corsair's mind, and discovers he is Cyclops' long-lost father. The Starjammers want to trade the Crystal to D'Ken, so that they will get close enough to kill him, but they are double-crossed. Despite Phoenix's best efforts, D'Ken unleashes the Crystal's power and sucks himself, the X-Men and the Starjammers inside.
Phoenix Saga Part 5: Child of Light
Season 3, Episode 7 TV-Y7
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D’Ken gets pulled into the Crystal, and becomes one with the universe inside it. Phoenix explains that the Crystal will suck all of existence inside of itself and create a new, lifeless universe to replace the one that was destroyed. On Earth, Storm and other heroes try to restore order as life starts to collapse. D'Ken, seemingly limitless in power, easily fights off the X-Men until Phoenix restores herself to power and helps the others escape. Realizing what she must do, she takes the opportunity to kiss Cyclops goodbye, tell the X-Men she loves them, and telling them that the heart of life is love. Sealing the Crystal, she traps D'Ken inside and once more sacrifices her life by taking the Crystal and soaring into the heart of the Sun.
Savage Land, Strange Heart Part 1
Season 3, Episode 8 TV-Y7
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Sauron kidnaps Storm to the Savage Land in order to feed from her mutant energy. Separated from the rest of the X-Men, Storm is encouraged by Sauron to free her inner tempest of energy, awakening Garokk. Phoenix continues to be absent from the team as Xavier and Moira McTaggert study the bond between Jean Grey and the Phoenix on Muir Island.
Savage Land, Strange Heart Part 2
Season 3, Episode 9 TV-Y7
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Garokk fuses with the island's volcano and the surging planetary force below it. Realizing his mistake, Sauron absorbs Garokk's energy and becomes as strong as Garokk. Sauron defeats Garokk. Storm regains control over her vast powers and the X-Men return home.
No Mutant Is an Island
Season 3, Episode 10 TV-Y7
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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. She tells him that a wealthy man has decided to adopt all the mutant children, especially Rusty; his true intentions are to make them his army to kill all humans in order to create a world where mutants are accepted. Cyclops must stop him and save the mutant children. Cyclops returns to the mansion, and is stunned to hear that Professor Xavier's powers have found Phoenix alive and well and returned to Earth.
Obsession
Season 3, Episode 11 TV-Y7
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Archangel has become obsessed with destroying Apocalypse, who he blames for ruining his life. Beast finds an alternative to defeating Apocalypse. The X-Men trap Apocalypse in a force field, create a pod around it, and jettison it into the space; they then return to the X-Mansion.
Longshot
Season 3, Episode 12 TV-Y7
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Longshot, rebel from another world, tumbles into this world with no memory. It turns out that Longshot is on the run from Mojo, a maniacal inter-dimensional TV executive. Mojo uses Jubilee as a 'prize' to lure Longshot and the X-Men into a deadly contest which Mojo broadcasts 'live' to raise ratings. The X-Men eventually defeat Mojo.
Dark Phoenix Saga Part 1: Dazzled
Season 3, Episode 13 TV-Y7
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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. Wyngarde creates a passionate romance between himself and her. When the X-Men come to rescue Jean, they find her fighting alongside Wyngarde.
Dark Phoenix Saga Part 2: The Inner Cirlce
Season 3, Episode 14 TV-Y7
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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. When Mastermind tries to force Phoenix to kill Cyclops, she finally breaks free of the psychic controls on her, leaving the X-Men to fight for themselves. When Mastermind finds her on the roof, Phoenix reveals that he foolishly unleashed her dark side, and she allows him to see the universe through her eyes -- the eyes of a god. Mastermind's mind collapses and Phoenix unleashes her powers on New York City, declaring that the Dark Phoenix has been born.
Dark Phoenix Saga Part 3: The Dark Pheonix
Season 3, Episode 15 TV-Y7
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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. To re-energize, she flies up through the D'Bari Star System, passing a very surprised Shi'ar Star Cruiser crew. As they watch in horror, she feeds upon and destroys an entire star system. Jean Grey, now completely part of the Phoenix, returns to her childhood home, overwhelmed by too much emotion and too much power. The X-Men try to fight her, and Cyclops tries to reason with her, but Professor Xavier is forced to fight Dark Phoenix on the astral plane. Though he seems to win, he reveals the only reason he won was that the part of Jean Grey's mind that was still normal sealed the Phoenix away. Lilandra, now Empress of the Shi'ar, arrives to announce that the Phoenix must be destroyed.
Dark Phoenix Saga Part 4: Fate of the Phoenix
Season 3, Episode 16 TV-Y7
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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. Xavier reads Lilandra's mind and challenges her guard to the Duel of Honor that Lilandra cannot refuse for Jean Grey's life. The X-Men argue about whether defending the Phoenix is worth defending Jean. Lilandra and Xavier argue bitterly. On the Moon, the X-Men and the Imperial Guard fight. When the X-Men are defeated and Jean Grey can no longer maintain psychic control, the Phoenix breaks free and the X-Men are forced to fight her again. When Jean realizes that it is up to her, she uses Phoenix's powers to use the Shi'ar's weapons to kill herself. The Phoenix, now released, is brought back to its senses by Jean's sacrifice and uses its powers to take a piece of life from all of the X-Men to renew the fire of Jean's soul. Jean Grey is brought back to life, and the Phoenix disappears into the stars.
Cold Comfort
Season 3, Episode 17 TV-Y7
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Former X-Man Bobby 'Iceman' Drake is caught breaking into a top-secret government installation. The X-Men free him and take him to Xavier, who is sad that his former favorite pupil apparently has gone bad. Iceman broke in because his house was trashed and Lorna Dane was kidnapped. Later, he again breaks into the compound and the X-Men follow. When they get there it turns out that the government installation was a training ground for the X-Factor. Lorna Dane faked her kidnapping to join the X-Factor and start a new life.
Orphan's End
Season 3, Episode 18 TV-Y7
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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. It later comes to light that the Shi'Ar police officers are corrupt and are attempting to kill a witness under Corsair's protection. The X-Men defeat the corrupt Shi'Ar officers. Cyclops invites Corsair to stay for a while, hoping to clear things up, and Corsair accepts.
Courage
Season 3, Episode 19 TV-Y7
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The day Morph rejoins the X-Men, terrorists attack a top-secret, high-tech weapons factory; the alert interrupts his homecoming party. Morph and Wolverine investigate and discover that the Sentinels are back. Morph hesitates to fight the Sentinels and has a flashback of getting shot by a Sentinel. Eventually, he overcomes his fear and defeats them, but he leaves the X-Men in the end, saying he's not ready yet.
Sanctuary Part 1
Season 3, Episode 20 TV-Y7
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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 the X-Men arrive to investigate Magneto's intentions, Cortez blames Magneto's disappearance on them and accuses them of assassinating Magneto. When the X-Men try to escape, Gambit sacrifices himself and the other X-Men escape.
Sanctuary Part 2
Season 3, Episode 21 TV-Y7
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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 (Gambit included!) Meanwhile, Cortez is rescued from the descending asteroid by Deathbird... and Apocalypse
Love in Vain
Season 3, Episode 22 TV-Y7
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In a New Mexico desert, Wolverine witnesses the crash of a spaceship carrying horrific, alien bug-like creatures—the Family—which overwhelm him. Rogue reunites with her first boyfriend, Cody, who ends up being a part of the Family's plot to have Rogue become their new leader. The X-Men defeat the Family
Secrets, Not Long Buried
Season 3, Episode 23 TV-Y7
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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 Children of the Shadow hunt him down. When his powers return, Cyclops gets help from some mutants and defeats them
Xavier Remembers
Season 3, Episode 24 TV-Y7
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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. Jean Grey again traps Shadow King on the Astral Plane, and Professor X regains control of his body
A Deal with the Devil
Season 3, Episode 25 TV-Y7
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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. Once in the sub, Omega Red reveals his plan to use the missile to cause destruction. Rogue destroys the sub, rendering it unable to launch its warheads. The submarine sinks deeper into the ocean, leaving Omega Red trapped inside.