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.

"Turn of the Rogue": While on a school geology field trip, Scott and Rogue realize that the schoolmates they thought they could trust have other plans. Now the two will have to work together in order to survive their rocky situation.

"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.

"Middleverse": When Rogue and Nightcrawler inadvertently stumble upon the abandoned lab of a mutant called Forge, Nightcrawler is accidentally sucked into another dimension by one of Forge's inventions. Nightcrawler discovers that Forge himself has been trapped in the dimension since the 70s! It'll take the help of the X-Men to get them back to the present!

"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.

"Strategy X": When high-schooler Todd Tolanski starts exhibiting toad-like mutant powers, Mystique sees a perfect opportunity to get a spy into Xavier's institute. Meanwhile the X-Men recruit a new member as Kurt Wagner joins Xavier's school to learn to harness his mutant powers.

"The X-Impulse": When Kitty Pryde discovers her mutant ability to phase through objects, she's naturally frightened and confused. Life proves to be more difficult for Kitty when both Jean Grey and Lance Alvers, a.k.a. Avalanche, approach her. While Jean tries to recruit Kitty to Professor Xavier's Institute, Alvers has plans of his own. Meanwhile, Sabretooth, Wolverine's arch-nemesis, rolls into town and he's looking for a fight!

"X-Treme Measures": When the Morlocks create a new sports drink that's harmful to mutants, it finds its way into Spyke's hands at a Skateboarding Competition. To make matters worse, Spyke's powers are becoming more and more uncontrollable and his temper is following suit. Meanwhile Kitty learns to drive, horrifying her worried fellow mutants.

"Blind Alley": While the X-Men work to restore Xavier's Institute after its devastating destruction, Mystique manages to break free of her incarceration. She soon sets a plan in motion that leads Cyclops into a deadly trap.

"The Stuff of Villains": When the Brotherhood is expelled from school with nowhere else to go, Magneto sends Gambit to get them to join his side. Meanwhile, Wanda gets her brother Pietro arrested and Magneto sends Gambit and his new recruits to break his son out of jail.

"Mainstream": Now that the world knows about mutants, Professor Xavier urges the X-Men and the Brotherhood's return to school to convince their peers they pose no threat. However, the school's Principal Kelly has other plans for the student mutant population.

"The Stuff of Heroes": Storm and Beast step in front of the Senate and try to curb rampant anti-mutant racism. The X-Men fight have to stop Juggernaut, who was unleashed by Mystique and is threatening to destroy a dam.

"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.

"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 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.

"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.

"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.

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

"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.