While Toad makes an attempt for infiltration of the Xavier Institute for gifted youngsters, which is basically a school for young mutants, a new mutant, named Nightcrawler, comes to the institute.
Kitty Pryde is a young Mutant, who was gifted with the ability to walk through solid objects. However, this gift grabs the attention of Lance, also known as Avalanche, who wants to use Kitty's gift to cause havoc in the school, and he hopes to also use her to cheat in school.
A young woman, who finds herself being called Rouge, leaves everything in her life behind when she realizes that she has become a danger to everyone around her. The X-men try to recruit her to become one of the newest members of their team, but that is not as easy as it looks, as Mystique takes upon the identity of everyone in the X-men, causing them to attack Rouge, so that Rouge will think the X-men are bad, and go with Mystique instead.
While at a Monster Truck rally, Logan and Jean notice a mutant with the gift of being super strong as well as being very big. Jean then in counters the mutant at Bayville High, and the mutant begins to crush on Jean. When Jean trys to run away from Blob, Blob knocks her unconscious, and takes her captive. Can the X-men save Jean from the Blob?
Evan Daniels and Pietro are school mates who are always at each other's throats trying to find out who is better. But when they learn about their powers it raises their level of competition to a dangerous level.
Nightcrawler gets caught between dimensions after activating one of Forge's old pieces of equipment.
Some students at Bayville High are going on a field trip, and Rouge ends up taking Jean's place. While on that adventure, Rouge and Scott learn that the people they respected the most have been lying to them.
Spyke needs extra credit in one of his classes, so he carries a digicam around to record his life and what makes it special. Problem is, Sabertooth then learns the location of the institute because of this.
The X-men and The Brotherhood are on a camping trip to get some survival training. However, while they are on that trip, Mystique brings Charles's brother Juggernaut to the institute to steal a high tech piece of equipment.
Nightcrawler learns his birth mother's identity, problem is, he doesn't want it to be true...
Wolverine travels to Canada to learn about project Weapon X, the reason why he has metal bones. However, things get bad when Nightcrawler and Shadowcat stowaway.
Scott learns that he has a brother after 10 years of not knowing about it. Meanwhile a fight breaks out between the X-men and their enemies.
Magneto's ultimate plan for Mutant-kind begins on Asteroid-M. Can the X-men and their allies stop Magneto?
Scott thinks that the X-men should tell everybody about their powers, but the Brotherhood decides to go public in their own special way and their way puts lives at stake.
Tabitha Smith, a.k.a Boom-Boom is having trouble fitting in with the X-men since she follows her own rules. She then must decide to stay with the X-men, or the Brotherhood.
Jean's powers begin evolving at an un-normal rate, and when they finally go berserk, it's up to the X-men to save her from destroying everything.
When Professor X must be away to stop Juggernaut from escaping and the kids do what any normal kids would do, they throw a party at the mansion inviting a bunch of school friends over. It's all going well until one special guest with great computer skills hacks Cerbero and the Danger Room.
Hank McCoy has used science to successfully fight his own mutation, but the formula isn't enough anymore and he becomes the Beast. Can the X-men save McCoy from doing something he'll forget?
Scott takes a trip to Hawaii to visit his brother and while surfing, Scott's brother is pulled out to sea by a riptide, forcing them to face the elements. Alone.
Storm begins to get attacked by "Shadow People" causing her sanity to be questioned. However, is it really all in her head?
Lance decides to become an X-men member in order to become more close to Kitty Pryde. However, he is not well-liked by most of the members, and he is blamed for everything that has been going wrong at the mansion lately. However, it turns out that it is all of the new recruits that are taking the vehicles out for a joyride, and not Lance, however, will they believe him?
There is a new vigilante in New York city that is keeping the streets safe. The vigilante seems to be well-liked by the citizens of New York... that is... until Magneto frames him. Now, Angel decides to get revenge on Magneto.
A powerful new enemy, who can bend minds, becomes a problem when he uses some of the X-Men to do his bidding. With the others being brainwashed, it's up to the rest of the X-men to take down this mind bender and free their friends. But what does Mesmero plan to do with the items that the X-men stole for him?
Forge's new idea how to help Nightcrawler goes awry during the Bayville high girls choice dance. Professor X and Forge want to learn more about this dimension that Kurt keeps teleporting to every time he teleports to another location. So, in order to learn more about the dimension, Wolverine and Nightcrawler must go through it, exploring it... But that might not be as easy as it sounds, as there are dinosaur like creatures ready to attack them, and many other vicious creatures waiting to destroy them.
Beast takes some of the younger X-men on a camping trip, so that they can get out of the Mansion for a change. However, things take a turn for the worst, when a scientist believes that Beast is Big-Foot, and captures Beast. It is now up to the other X-men to find and save Beast.
Jean is tired with Scott trying to be the "hero" all of the time, so the X-girls hook up with Boom-Boom and trash the rules. However then end up getting in over their heads, and must work together with Scott and Nightcrawler to get out of this mess that they're in.
Something very important has been stolen from S.H.I.E.L.D and Wolverine has personal ties to it from his past in the military working alongside Captin America. Now Wolverine, Rogue and Nightcrawler must stop Magneto from using the project to make himself much more powerful.
Mystique has returned once more to take control of the Brotherhood again. But it turns out that she did not return all by herself...
The X-Men join with their rivals The Brotherhood, forcing one member of the X-Men to leave the group.
The X-men and The Brotherhood go face to face with Magneto's group of mutants.
The Brotherhood and The X-men team up, under the leadership of Mystique to find their captured comrades. Banded together, the two teams must enter Area 51 and free their teammates, however they must do that and fight the army at the same time...
Juggernaut goes on a rampage and the X-Men still have no clue where to find their leader. Can they defeat Juggernaut without the psychic blasts of Charles?
The X-men teenagers are granted the opportunity to go back to high-school, and prove themselves. However, they must do that without using any of their super-powers. However, this may not be as easy as it sounds, as Principle Kelly has enrolled the Brotherhood, hoping to cause the X-men to use their powers, so that they'll get kicked out of school...
Mystique is trapped in Area 51, causing the Brotherhood of Mutants to be leaderless once again. However, Magneto decides to go after this group, hoping to take control of the Brotherhood of Mutants, and make them his new team...
Mystique ends up breaking out of Area 51. After her escape, she goes after Cyclops, the man that caused her to be in the hands of the United States army. Can Cyclops survive Mystique's attack on him?
Spyke's mutation is becoming harder to control, as well as his temper. He finally finds solace and acceptance in a most unlikely place -- but at what cost?
As Wanda continues the search for her father, Toad goes to extremes to try and get her to fall in love with him.
All the personalities Rouge had consumed over the years begin taking over, and she becomes a danger to everybody, so it's up to the X-men to save her.
When the second key to unlock Apocalypse is found, the X-men find themselves in a battle against the Acolytes. The X-men want to protect it, while the Acolytes want to destroy the key. But what happens when the key is destroyed?
A new Weapon X has been created using his genetic code. Her name is X23, and she arrives at the Institute in search for a fight against Wolverine.
Mesmero takes control of Rouge's mind and has her steal the powers of all the X-men, the Brotherhood, and the Acolytes. Then, Mesmero, Mystique, and Rouge head for Tibet, to unlock the final door that is keeping Apocalypse from breaking free. Now, the X-men and the Acolytes must fight side-by-side in order to take down the coming threat of Apocalypse.
While trapped in a pyramid, that was supposed to be Apocalypse's resting place, Professor X learns the history of Apocalypse. However, it turns out that the X-men and the Acyoltes went to the wrong place, leaving Wolverine, Sabertooth, and Gambit to fight Rouge, Mystique, and Mesmero in order to keep them from freeing Apocalypse... But will they succeed?
Some of the various members of the X-men team take a cruise to get away from all of the mutant propaganda that has been plaguing them lately. However, the X-men have to expose their secrets to save a small village from getting destroyed by a volcano.
Magneto decides to take a stand against Apocalypse, even though the X-men don't want him to. Is Magneto powerful enough to handle Apocalypse though? And Rogue will have to face one of the hardest decisions of her life. Evolution will never be the same again!
The Brotherhood has supposedly turned over a new leaf, and has begun to fight crime. However, how long until their true colors begin to show?
Wolverine faces X23 once again, and X23 isn't too happy about it. She wanted to get over her past, but looks like that won't happen now. Can Wolverine protect X23 from falling into Hydra's hands?
Professor X's past comes back to haunt him as the son he never knew he had is discovered. What does David want with the Professor, and can the X-Men handle the powers of this new mutant?
With Mutant-hate-crimes beginning to become a real problem in Bayville, Spyke returns more powerful than ever. However, he is not the only one to return, but Duncan Matthews does as well, causing all kinds of trouble for mutants.
Gambit needs help rescuing his father, so he tricks Rouge into going to New Orleans with him.
When Kitty is saved by a girl who just disappeared, she learned that it was just a dream. But who is this Danielle?
After Professor and Storm are "killed" by Apocalypse, the X-men must gather all of their teammates and allies in a fight that will decide the fate of human and mutant kind forever. However, it's not just a battle against Apocalypse, but a battle against each other when they find out that Magneto, Mystique, Professor Xavier, and Storm have become Apocalypse's four horsemen.
The X-men, Brotherhood, and Acolytes only have a short amount of time till Apocalypse completes his master plan. Wolverine, Nightcrawler, and Cyclops find themselves in a battle with Mystique, the mutant that is guarding Apocalypse. Can they get through in time to stop Apocalypse? Meanwhile the other mutants face off against their former allies, can they hold their own while Wolverine's team takes out Apocalypse?