Fabian Cortez kidnaps Jubilee because Apocalypse is trapped in 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.
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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.
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.
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.
In Victorian London 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.
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 with her 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.