"Beast of Bayville": Dr. Hank McCoy has no energy left to fight his mutation, which forces him to be a violent Beast. When he finally becomes a monster, Spyke is the only one who can possibly reach Dr. McCoy.

"Shadow Dance": The Bayville High Sadie Hawkins dance arrives, and everybody is scrambling for dates. Jean is highly jealous of Scott's date. In the meanwhile, Forge constructs a device which augments Nightcrawler's teleportation, but is unaware that vicious monsters from Kurt's bamf dimension will now be able to enter Earth.

"Retreat": In order to help a depressive Beast out of his slump, Kitty arranges a field trip with the New Mutants. However, hunters catch Beast, thinking him to be Bigfoot, and the young mutants must save their teacher from life in captivity.

"The HeX Factor": A mentally unstable, but immensely powerful mutant called Wanda is abducted from a mental institution and becomes the newest Brotherhood member, much to the horror of her brother Pietro. The new Brotherhood defeats the X-Men single-handedly.

"Power Surge": Jean Grey loses control of her powers, and the only one able to contain her is Rogue.

"Fun and Games": While Professor X has to mend Juggernaut's stasis cell, the younger X-Men trick Cyclops and Jean Grey to exit the Mansion in order to have a party. However, there is a guest with sinister intentions.

"Adrift": When Cyclops and Havok are on a boat tour, a great storm comes and nearly kills them.

"African Storm": Storm is tormented by Houngan, an evil African shaman who wants to take over Africa. Storm and the X-Men have to stop an enemy who knows every weakness of hers.

"Joyride": Lance Alvers (Avalanche) wants to join the X-Men in order to be near Kitty. Unfortunately, the rest of the Brotherhood, along with several of the X-Men, are not pleased with his decision.

"On Angel's Wings": In Christmas time, a mysterious angel is saving people's lives. Rogue and Cyclops track down Warren Worthington, who is deeply unsure about his mutation. Magneto wants to frame him, in order to instill hate against mankind into him, and the two X-Men have to set things straight.

"Mindbender": A mysterious hypnotist named Mesmero kidnaps some of the X-Men and brainwashes them into committing crimes for him.

"Walk On The Wild Side": The female X-Men are fed up with playing second fiddle, and form a vigilante crime-fighting group. For a while, things go great, but in the end, an old enemy crosses their way.

When Professor X sends a mission to destroy the mutant registration files, things go terribly wrong and the X-Men must cope with the heavy price of fighting for mutant equality.

Magneto, Professor X's old friend and new enemy, has returned and is preparing to launch nuclear missiles in order to ensure a war between mutants and humans.

"SpykeCam": For a school project, Spyke gets a video camera to document life as a teenager. While Spyke videotapes his fellow X-Men, Sabretooth decides the video camera is the perfect way to find Wolverine and Xavier's School along with it.

"Speed and Spyke": When Storm's nephew, Spyke, begins to develop his mutant powers, he decides he'd rather use his unusual abilities for revenge against a thief calling himself Quicksilver, rather than learn to harness his powers at Xavier's Institute.

"Rogue Recruit": After a young mutant named Rogue touches a fellow student and absorbs his energy and memories, she runs away from home, confused and frightened. Now it's open to Professor Xavier and his students to recruit Rogue and help her before Mystique can turn her against the X-Men.

"Growing Pains": The Brotherhood gatecrash a soccer match of Jean's team and threaten to expose mutantkind to the world.

"Day Of Reckoning" Part One: Anti-mutant racist Bolivar Trask abducts Wolverine and introduces him to his newest invention, the Sentinels. Meanwhile, Magneto wants to provoke all-out war between mankind and mutantkind and summons his Acolytes to create mayhem.

"Day Of Reckoning" Part Two: The X-Men are shocked when Professor X teams them up with the Brotherhood to stop them, but then, a shocking twist reveals that nothing was to be as it seemed to be.

"Day Of Recovery": The remaining X-Men and Brotherhood members go to Area 51 to save their captive members. However, when Cyclops traps the treacherous Mystique in Area 51 to blackmail her into saying where Professor X is, the squads split. The X-Men are now alone in a world which shuns them.