Kurt becomes trapped in an alternative universe created by another young mutant known as Forge, who himself has been stuck there for more than 20 years.
Scott Summers and Jean Grey prepare for their geology club excursion, but Mystique has different plans in mind, replacing Jean with Rogue in an attempt to put further distance between her and the X-Men.
Spyke receives a video camera for a class assignment, but the camera is found by Wolverine's nemesis, Sabretooth, who uses it to find out where the Xavier Institute is in order to hunt down his rival, Wolverine.
While the X-Men and Brotherhood are at a survival training camp, Mystique releases the unstoppable Juggernaut. But when the unstoppable mutant threatens both teams, the X-Men and Brotherhood must work together in order to stop him.
Wolverine's tortured origin comes back to haunt him. In the Canadian wilderness, he runs into not only his arch rival Sabretooth, but also the doctor who gave him his Adamantium skeleton who still has insidious plans for him.
Scott finds out his younger brother Alex Summers, who he believed dead, is alive and maybe soon recruited by Magneto to join him as the X-Men are forced to fight the Brotherhood for a place in Magneto's sanctuary.
Magneto holds multiple battles to find out which mutants are "worthy" of joining him on Asteroid M. Where Magneto offers to greatly strengthen and increase the mutant abilities of the winners to their full and maximum potential.
When Scott and Kurt use their powers to save several people, the question of how to keep their powers a secret comes up. Professor X maintains that the world is not ready to know about them. However, the Brotherhood, have other ideas.
After being grounded for reckless behavior during a training mission, Tabitha doesn't need her father asking her to steal money for "her mother". Kurt develops a crush on Boom Boom because of her carefree spirit and adventurous nature.
Jean Grey's telepathic and telekinetic abilities start growing in sudden bursts. At first she tries to ignore it, but with each burst she has increasing trouble regaining control. Meanwhile, the school gets a new science/phys. ed. teacher.
When the Professor, Wolverine, and Storm are away on personal matters, the younger X-Men decide to have a party at the mansion, but a nerdy schoolmate discovers The Danger Room and thinks it's an elaborate video game.
Henry McCoy, a teacher at Bayville High (and a former student of Xavier's) undergoes a strange transformation into a violent and angry blue-furred beast. Spyke is the only one who can possibly reach Dr. McCoy.
Alex gets pulled out to sea by a riptide while surfing using a surf board fitted with a webcam. Scott attempts to rescue his brother, but a huge storm threatens both their lives and they must face the elements on their own.
When an evil African shaman comes to the institute to steal Storm's weather controlling powers while planning to use them to take over Africa, Storm is faced with the decision to send Evan back to his parents.
Lance Alvers wants to join the X-Men to be closer to Kitty. Unfortunately, the rest of the Brotherhood are not pleased with his decision and Lance has trouble fitting in, when he becomes the prime suspect for several recent joyrides.