The X-Men are an elite team of mutants, genetically gifted human beings with superpowers, sworn to fight for mutant rights against hostile Government agencies, whilst at the same time protecting mankind from mutant supremacist Magneto who seeks to destroy the human race in return for the atrocities committed against mutant kind.
Rushing to investigate a disturbance downtown, the X-Men find Sabretooth on the rampage again, but realize too late that it isn't really Sabretooth at all. It is the Phalanx, a voracious alien life-form that can assume the guise of anything or anyone. Before long, the X-Men are all captured, except for Beast, who must find a way to stop the alien horror from devouring the entire Earth.
Snatched from the jaws of the Phalanx by the villainous Mr. Sinister, Beast and Forge search for allies to help them battle the alien threat. Gathering assistance from such unlikely sources as Magneto and Sinister himself, they embark upon a daring and risky plan to free the planet from the clutches of the Phalanx by traveling straight into the belly of the beast.
The former Soviet Union's living weapon, Omega Red, is thawed out by the US Military to deal with an abandoned Soviet nuclear submarine near Hawaii. He asks for his old enemy, Wolverine, and the woman responsible for freezing him most recently, Storm, to accompany him on the mission. Omega Red is offered restored humanity, but once aboard the warhead-filled sub, he reveals his true, deadly intentions.
Cyclops, still in mourning after Jean Grey's "death", quits the X-men and returns to his orphanage home and encounters his friend Sarah. She tells him that a wealthy man has decided to adopt all the mutant children, especially Rusty, but his intentions are to make them his army to destroy all humans in the world so that mutants are accepted. It's up to Cyclops to stop him and save the mutant children. Later, Cyclops returns to the mansion and he and the other X-men discover that Jean Grey hasn't died after all.
Longshot, a rebel from another world, tumbles into this world with no memory and a murderous gang led by the six-armed woman warrior Spiral hot on his trail. It turns out that Longshot is on the run from Mojo, maniacal inter-dimensional TV executive. Using Jubilee as the 'prize', Mojo and his minions lure Longshot and the X-Men into a deadly contest which Mojo broadcasts 'live' to up his ratings.
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 -- she has never known her birth parents and feels pretty hostile toward them, whoever they are. 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. There are more 'bloodlines' here than anyone imagined, including the Friends of Humanity who arranged this 'reunion' in the first place.
The dashing alien, Arkon, unleashes terrible weather conditions over Washington D.C. to get Storm's attention. It works, he begs her to return with him to his planet, Corsus, to save it from meteorological chaos which threatens his people. After much pleading, Arkon convinces Storm. Intrigued by this dynamic leader but slightly suspicious, Storm departs but leaves a clue for the other X-Men to follow. The X-Men travel through an inter-dimensional portal and arrive to 'rescue' Storm, just as she is in the midst of restoring the planet's raging eco-system. Once successful, Storm is proclaimed savior throughout this universe. What's more, Arkon asks her to marry him.
Spectacular preparations for Storm's wedding to Arkon proceed quickly. But as Jubilee helps Storm, the new queen, prepare for the wedding, Jubilee can't help notice how badly the palace workers are treated. When Storm mentions this to Arkon, he reminds her she is new to his world, and asks her for her trust. meanwhile Wolverine, Cyclops and Beast discover there are fleet ships bringing slaves from the neighboring planet. Arkon, it seems, is a ruthless tyrant. Storm must know the truth. Back at the castle, Storm has been making a few discoveries of her own.
Jubilee tells children her own fairy tale having herself, her fellow X-Men and their greatest enemies be the characters in it.
Fabian Cortez helps Apocalypse escape from the astral plane.
Wolverine thinks back to the time when he fought during World War II and teamed up with Captain America.
The origin of Mr. Sinister.
When the army learns of Sam Guthrie's cannonball power, they try to enlist him in their ranks.
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.