As Kurt Wagner (Nightcrawler) adapts to his new home at the Xavier Institute, Mystique attempts to spy on the facility with a young boy who has toad-like powers.

Kitty Pryde discovers her mutant abilities of phasing through solid matter. Xavier sends Jean Grey on a mission to recruit her as one of the X-Men, only to find out that she has already been won over by Lance Alvers, otherwise known as the mutant Avalanche with the ability to cause earthquakes and tremors.

When Rogue accidentally triggers her mutant ability by absorbing a local boy's memories, strengths, and abilities via mere skin contact, the X-Men head off to Caldecott County, Mississippi to recruit her. However, Mystique isn't willing to let her out of her sights because she wants her daughter to become one of them, so she and Destiny get to Rogue first to convince her that X-Men are hunting her down.

Fred Dukes (Blob), a former sideshow entertainer from Texas, gets enlisted by Mystique into Bayville High. But his short temper and blubbery girth prevents him from making any necessary friends. He does get some help from Jean Grey in finding his way around the school, but things take a turn for the worse when he mistakes this for romantic love.

Evan Daniels, Ororo Munroe/Storm's nephew, is exhibiting his mutant ability of projecting a multiple of boned spikes and projectiles. Despite knowing his mutant abilities, Evan's initially refuses to join the X-Men. However, when former basketball teammate Pietro Maximoff (Quicksilver) continually steals money from him (along with getting him in trouble), Evan accepts the offer in an attempt to take his former friend down.

One day, Kurt's childish behavior clashes with Scott's dead seriousness once too often. Later, Kurt (in his true form) accidentally activates a device which transfers him to a parallel dimension. There, he meets Forge, who had been trapped there since the late seventies, and together, they devise a plan to break out and return to their normal dimension. Things get complicated when the other X-Men discover the device and the Brotherhood then tries to steal it from them.

The X-Men and the Brotherhood battle each other in a summer camp, but must cooperate when a large and unstoppable mutant named Cain Marko (Juggernaut) threatens both Charles Xavier and Mystique.

Scott is reunited with his younger brother Alex, who is recruited by Magneto to join him as the X-Men are forced to fight the Brotherhood for a place in Magneto's sanctuary.

The Brotherhood (minus Mystique) gatecrash the girls' championship soccer match (in which Jean's team is taking part) and threaten to expose mutantkind to the world.

Jean Grey suddenly loses control of both her strong telepathic and telekinetic abilities. And the only one who can stop her psionic abilities from further going haywire is Rogue.

While Professor X has to mend Juggernaut's stasis cell, the younger X-Men trick Cyclops and Jean Grey into leaving the Mansion in order to have a party. Note: First appearance of Arcade. Also in this episode, Risty is revealed to be Mystique.

Dr. Hank McCoy has no strength left to fight his bestial mutation, which forces him to be a violent and angry Beast.

During Christmas time, a mysterious angel is saving lives. Rogue and Cyclops track down Warren Worthington, who is deeply unsure about his mutation.

A mysterious hypnotist named Mesmero kidnaps some of the X-Men (Jean Grey, Spyke, Nightcrawler and Kitty Pryde) and brainwashes them into committing crimes for him.

The Bayville High Sadie Hawkins dance arrives, and everybody is scrambling for dates. While this is going on, Forge constructs a device to greatly strengthen and magnify Nightcrawler's teleportation abilities to the point where he teleport across much longer and greater distances, however the demonic creatures he encounters while passing through a separate dimension during his teleporting, manage to escape through open portals Nightcrawler leaves behind.^[5]

Nick Fury informs Wolverine that Magneto has stolen a device once used to create the super-soldier Captain America. Wolverine, Rogue (who knows the location, having absorbed Magneto's memories in "On Angel's Wings") and Nightcrawler (whose teleporting capabilities are able to get him inside Magneto's base) go to recover it.

Mystique returns to the Brotherhood with a mentally unstable, but immensely strong and powerful mutant named Wanda Maximoff, much to the horror of her twin brother Pietro.^[5]

Note: First appearance of Scarlet Witch and Agatha Harkness.

Anti-mutants activist Bolivar Trask abducts Wolverine and introduces him to his newest invention, the Sentinels. Meanwhile, Magneto wants to provoke an all-out war between humans and mutants, and summons his Acolytes to create mayhem.^[5]

The X-Men are shocked when Professor X teams them up with the Brotherhood to stop Magneto, but then, a shocking twist reveals that nothing was as it seemed to be.^[5]

The remaining X-Men and Brotherhood members go to Area 51 to rescue their captive members. They team up with the Brotherhood and Nick Fury points them in the right direction, they save the others, but Cyclops leaves Mystique behind.^[8]

Despite rescuing Professor X, the bigotry towards mutants still exists as our heroes return to Bayville High, scorned and verbally abused by their human classmates, including their mutant-hating Principal Edward Kelly. Also, the School Board decides whether or not to allow mutants to attend school. However, Kelly enlists Duncan to team up with the Brotherhood (Avalanche, Toad, & Blob) to ensure a permanent mutant ban.^[8]

Wanda wants to find out where her father Magneto is, so she enlists Caliban for help. She then goes to her brother Quicksilver for info. When he refuses, Wanda delivers him to the police. When the Brotherhood tries to break him out of a prison transport (as part of Magneto's offer from Gambit), Rogue and Shadowcat appear to break up their rescue operation.

Jean is about to confess her strong and deep mutual romantic love to Scott when Mystique (who managed to escape from Area 51 and is out for revenge) abducts Scott and abandons him in the desert in Mexico without his ruby quartz glasses. Jean, who has vivid telepathic visions of him in peril, tracks him down, but Mystique is determined to kill them both.^[8]

Spyke joins a skateboarding contest sponsored by "Pow-R 8" soda. However, Pow-R 8 is harmful to mutants, and when Spyke drinks a swig, his mutation greatly advances, poisons, and disfigures him seriously. He is saved by the Morlocks, and in the end, Spyke joins them.^[8]

Wanda tracks down Magneto to his Acolyte headquarters in a nearby ski resort. Meanwhile, Kurt is spending time with Amanda Sefton and meeting her parents. In a bid to win Wanda's affections, Toad steals Nightcrawler's image inducer (thereby blowing his cover in front of the Sefton household) and pursues Wanda, followed by an angry Kurt. However, when Wanda gets abducted by Magneto and is brainwashed by Mastermind into believing her father was a kind and giving man (erasing her memory of the asylum she was sent to), the two team up to rescue her.^[8]

Rogue witnesses her infatuated crush, Scott, date Jean. She is consoled by her British friend, Risty, but when she accidentally touches and absorbs everything from her at a concert, she finds out that she was Mystique all along in disguise. Absorbing Mystique's power, Rogue's alter-egos from inside that she has absorbed in the past, use the shape-shifting ability she accidentally borrowed from Mystique to break free from Rogue's inner self, fighting to take control over her body and mind. Thinking everybody hates her, Rogue's latent multiple personality disorder breaks through and she loses her sanity. The X-Men have to stop their friend and colleague, who has all of their mutant abilities combined and in the verge of burning herself out.^[8]

Angel spots Gambit stealing a mysterious artifact, but when he tries to stop him, Mesmero fights him off. When the Acolytes want to steal another artifact, the X-Men fight them and discover there is a bigger plan happening. Soon both teams face a spider-like being which is virtually unstoppable. Magneto and The Acolytes destroy the spider-like creature. However, it was actually a guardian to prevent Apocalypse's release and now that it is destroyed, the second gate will open.

Taking a break from superhero duty, the X-Men (without Rogue and Berzerker) take a pleasure cruise. But Magma becomes violently ill, literally suffering from earth withdrawal. When Boom Boom and Iceman take her to an island, she accidentally triggers a volcano. When the volcano threatens to explode again, Magma dives into its heart to silence it once and for all.^[8]

A mysterious female assassin terrorizes the X-Mansion, knocking out the X-Men one by one. Wolverine finds out that it is his clone, created by Dr. Deborah Risman and raised without love by HYDRA, and she wants to kill him because she holds him responsible for her miserable life. Wolverine and X-23, as she is called, square off in a battle that Wolverine does not want to win.^[8]

Rogue falls under the mind control of Mesmero and is used as a weapon to absorb the mutant powers of every member of the X-Man, the Brotherhood of Mutants and the Acolytes. The three factions reluctantly cooperate and find out that Mesmero wants Rogue to give all of her stolen powers to Apocalypse to awaken him.^[8]

A strange phenomenon occurs in the wake of Apocalypse: A jungle-covered Mayan pyramid takes on a technological appearance and an impenetrable force shield surrounds it, even down into the ground underneath. The X-Men receive permission from the government there to study the base. However, Magneto, in an act of revenge, makes an attack upon it. Meanwhile, Nightcrawler tries to revive his mother Mystique who is still trapped in stone, much to the dismay of Rogue.

After being kidnapped by Omega Red, Wolverine manages to escape to a nearby forest. There he finds his clone, X-23, on a personal mission to destroy the person responsible for creating her: Madame Hydra. Now, the two team up to take on Hydra and destroy the Hydra base. Meanwhile, Cyclops and Jean Grey try to teach the New Mutants much more advanced ways of using their mutant abilities.

Charles Xavier's son David has been seemingly abducted. Charles, Storm, Cyclops, & Jean Grey track him down in Scotland, and it turns out that he suffers from multiply identity disorder, and that his hidden malicious personality, (born out of his hatred and agony for his father and his evil will), called Lucas, is overwhelming him. Meanwhile, Kitty and Kurt have some not so good adventures while they're ill with the flu, as Kurt teleports involuntarily as he sneezes in his sleep.

Spyke makes his return, having turned into an angry vigilante who protects the Morlocks. He is unafraid to go in public with his disfiguring mutation, causing panic in his environment, especially since the extreme prejudice against mutants is on the rise. Anti-mutantists Duncan Matthews and his friends go and hunt Spyke down, and they even stumble upon a small boy named Dorian Leech. Also, in a foreshadow towards the eventual fight against Apocalypse, Nick Fury of SHIELD releases Bolivar Trask and orders him to build new improved Sentinels.

Kitty meets Danielle Moonstar and they quickly become friends. But she wakes up the next morning and realizes that she (seemingly) dreamed everything up. Strangely, it appears that Kitty's dreams had a deeper meaning, leading into a race-against-time search as she tries to find her new best friend.

Apocalypse plans to turn all humans with the dormant X-gene into mutants, while killing those who aren't strong enough. He has turned Magneto, Professor X, Storm, and Mystique into his Four Horsemen, and has covered the world with a network of energy pyramids to stage his plan.

In order to prevent all humans from being turned into mutants, the X-Men, the Brotherhood of Mutants, S.H.I.E.L.D., the Acolytes, Angel, Spyke, Havok and the New Mutants all join forces to save humanity from the ambitions of Apocalypse. Rogue defeats Apocalypse at the last minute by borrowing Leech's ability to cancel other mutant abilities. She stops the pyramids' energy and closes his case with Apocalypse still inside. Wolverine helps, sending him back through time. In the end, Professor Xavier shares his visions of the future while he was under Apocalypse's mind control:

• The discrimination and persecution of mutants continues
• Magneto as teacher of the New Mutants
• The Brotherhood working for S.H.I.E.L.D.
• Jean eventually gets possessed by the almighty Phoenix Force; becoming the Dark Phoenix.