The Best Episodes of X-Men: The Animated Series
They are mutants, genetically gifted human beings - the world's newest and most persecuted minority group. Amidst an increasing climate of fear and bigotry, one enlightened individual, Professor Charles Xavier, has created a safe haven for some of these powerful outcasts. The mutants here are taught to harness their unique abilities for the betterment of the human race. They fight against hostile Government agencies and mutant supremacist Magneto, and his factions, which seek to destroy the human race.
#1 - The Dark Phoenix Saga (Part 4): The Fate of the Phoenix
Season 3 - Episode 14
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.
#2 - Graduation Day
Season 5 - Episode 14
Due to a serious injury, Professor Xavier is dying and must leave with Lilandra and go with her to the Shi'Ar Empire. He bids farewell to his X-Men. The last scene of this show ends with all of the X-men standing outside the mansion watching Lilandra's ship carrying Xavier flying away.
#3 - Courage
Season 4 - Episode 3
Morph feels he's finally ready to return to the X-Men. But his homecoming is interrupted by the return of the Sentinels, the robotic mutant-hunters who nearly killed him the last time he faced them. Will history repeat itself?
#4 - Phoenix Saga (Part 2): The Dark Shroud
Season 3 - Episode 4
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.
#5 - Obsession
Season 3 - Episode 10
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.
#6 - The Juggernaut Returns
Season 3 - Episode 17
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.
#7 - Phoenix Saga (Part 4): The Starjammers
Season 3 - Episode 6
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.
#8 - Beyond Good and Evil (Part 2): Promise of Apocalypse
Season 4 - Episode 9
When Oracle, the psychic member of the Imperial Guard is kidnapped by Apocalypse, Professor Xavier deduces his scheme involves capturing mutants with telepathic abilities. The X-Men are split up to track them down before the villains can, which puts Wolverine & Shard in the middle of a scuffle between Archangel and a ninja named Psylocke.
#9 - Phoenix Saga (Part 5): Child of Light
Season 3 - Episode 7
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.
#10 - The Lotus and the Steel
Season 4 - Episode 13
Finding himself continually losing control, Wolverine takes a sabbatical to Japan, in an effort to find inner peace in temple-building. Instead, he faces a village under siege by a group of bandits, and struggles to help them without compromising his search for his true nature.
#11 - Beyond Good and Evil (Part 4): End and Beginning
Season 4 - Episode 11
Two of Apocalypse's former evil allies, the captive Wolverine, the loose cannon Cable, and the exiled Bishop, come together to free the kidnapped psychics and save reality from being rewritten.
#12 - The Dark Phoenix Saga (Part 1): Dazzled
Season 3 - Episode 11
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.
#13 - Beyond Good and Evil (Part 3): The Lazarus Chamber
Season 4 - Episode 10
After swiping the government's own time machine, Cable ends up recruiting the X-Men on his mission to destroy Apocalypse's source of immortality at its creation.
#14 - Phoenix Saga (Part 3): Cry of the Banshee
Season 3 - Episode 5
Professor Xavier's claims of the capture of his alien soulmate Lilandra by Juggernaut and Black Tom Cassidy are met with skepticism.
#15 - A Rogue's Tale
Season 2 - Episode 9
Haunted by visions of a strange woman, Rogue must come to grips with the dark secrets of her past prior to joining the X-Men.
#16 - Time Fugitives (Part 2)
Season 2 - Episode 8
To stablize his own timeline, Cable comes to the present to prevent Bishop from saving mutant-kind from Apocalypse's plague.
#17 - One Man's Worth (Part 2)
Season 4 - Episode 2
Bishop, Shard, and the alternate-present versions of Wolverine & Storm, will have one more chance to save Xavier from being killed before he founded the X-Men... if they can survive the alternate-future ruled entirely unopposed by Mastermold.
#18 - Secrets, Not Long Buried
Season 4 - Episode 15
Cyclops heads solo to the desert town of Skull Mesa, where humans and mutants live in harmony, to visit an old mentor from his youth. But he not only finds himself powerless when he arrives, but discovers the place under the rule of a maniacal mutant, with none of the citizens willing to take a stand.
#19 - Beauty and the Beast
Season 2 - Episode 10
Beast falls in love with his patient, a blind woman named Carly, and though the feelings are mutual, her mutant-hating father and anti-mutant sentiment drive a split between the pair. Meanwhile, Wolverine seeks to take down the Friends of Humanity from the inside out.
#20 - Beyond Good and Evil (Part 1): The End of Time
Season 4 - Episode 8
Apocalypse steals Cable's computer in the year 3999, allowing him to time travel to the past, where he schemes to bring an end to his struggle against inferior mutants once and for all. This leads to Bishop becoming trapped amid the timestream, and brings
#21 - Days of Future Past (Part 1)
Season 1 - Episode 11
A mutant from more than half a century into the future, named Bishop, arrives in the present, attempting to change history for the better, by stopping an X-Man from committing an assassination. But between being chased by a future breed of Sentinel, and the details of his mission being fuzzy, he's got his work cut out for him.
#22 - The Dark Phoenix Saga (Part 3): The Dark Phoenix
Season 3 - Episode 13
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.
#23 - Xavier Remembers
Season 4 - Episode 16
Trapped on the astral plane after suffering a concussion, Professor Xavier is at the mercy of the Shadow King, and in desperate need of help from his X-Men, who are unable to hear him.
#24 - Phoenix Saga (Part 1): Sacrifice
Season 3 - Episode 3
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.
#25 - One Man's Worth (Part 1)
Season 4 - Episode 1
Bishop & Shard recruit Wolverine & Storm for a time travel mission to save Professor Xavier's life. Except they're from the parallel timeline where he died before founding the X-Men, a world where humans and mutants are in a constant war with one another. Not only do they pair lack a connection to him, but correcting history may put an end to their marriage.