15-year-old Kitty Pryde wakes up one day and finds herself able to walk though objects. She tries to ignore it, but finds that hard when she's approached by Jean Grey and a mutant trouble maker, who both say they know what she's going through and want to help her. Meanwhile Wolverine's old nemesis, Sabertooth, arrives in town - looking for trouble.
When Scott and Kurt use their powers to save several people from a car crash, the question of how much they're willing to ignore to keep their powers a secret comes up. Professor X maintains that the world is not ready to know about them, however the other mutants, now without Mystique's guidance, have other ideas...
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 the 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.
Magneto ruthlessly hunts Apocalypse, but the X-Men aren't so eager. When nothing can be done about Mystique, the professor gives her to the Brotherhood. Much to Rogue's objection, Kurt brings it back. When the two fight, Kurt sees a tear. Jean discovers Apocalypse in Mexico, and the professor, Cyclops, Jean, Shadowcat, Beast, & Wolverine go to investigate. They try to be peaceful, but Magneto attacks. Apocalypse defeats him with ease, and appears to kill him. Back in Bayville, Kurt has Wanda contact Agatha. Rogue finds the two meeting, and Agatha tells her that she's the only one who can save her mother. Kurt begs her to do the right thing, but Rogue knocks the statue off the cliff. It shatters before Kurt can teleport down to it, and Rogue just walks away.
When the Brotherhood saves a few people after Wanda accidentally causes a subway accident, they are regarded as heroes. The X-Men are utterly repulsed. The Brotherhood begins to cause accidents just to get famous. When the X-Men figure it out, Pietro tricks Wanda into using her powers to make it look like the X-Men are the villains. After the X-Men are arrested, the Brotherhood tries to cause one last accident. When they can't stop it, the X-Men are released to help. Shadowcat & Jean can't stop the explosion, so Avalanche does. He promises that there will be no more heroics.
David Haller, Xavier's son, who has lived away from his father's knowledge, contacts him seeking help. He has been kidnapped by a man called Lucas. Xavier, Jean, Scott and Storm travel to Scotland where Xavier's ex-wife lives with David and a street boy called Ian. When Ian leaves the house, Jean follows him and is kidnapped by Lucas. Scott tracks them to an old castle in ruins where teenagers throw parties and gets captured. Xavier and David's mother find Ian and with his help, they get to the castle and face the boys there while Jean, Scott and David escape. David meets his father for the first time, and he reveals he is actually Ian. Lucas, too, by turning into Ian first and later into Lucas. His multiple personalities change his appearence every time. Xavier enters in his son's mind trying to erase Ian and Lucas, but fails and Lucas is the only one left who disappears in the sky. Meanwhile, at Bayville, Kitty and Kurt are way too sick to go to school.
A further mutated Spyke, now armored and able to throw flaming spikes, now protects mutants, including Magma and Cannonball who are walking out of a library when Duncan pulls up and tries to attack them. Xavier is concerned and sends a reluctant Wolverine to talk to him, to no effect. Callisto is also concerned that Spyke's efforts will bring down the wrath of mutant-haters on the other Morlocks who can't protect themselves. Her predictions come true when Spyke's efforts set off further anti-mutant hysteria. Spyke protects a young mutant named Dorian Leach, who it is revealed to have the power to suppress energy - electrical, mutant, whatever. The Morlocks and the X-Men come to Spyke's aid, and defeat Duncan and his men. Dorian shows up and temporarily negates everyone's powers. Duncan is arrested and Spyke returns to the underground. Meanwhile, Apocalypse creates a second sphere in China which resist all efforts to destroy it, and Nick Fury is ordered to free Trask and have him reinit
Gambit kidnaps Rogue and tells her he is trying to help her to forget what she did to Mystique. When everyone notice she is missing, Wolverine sense Gambit's smell and goes to Magneto's base where he find Pyro and tells him the Acolytes are separated and he does not know where Gambit is. Gambit takes Rogue to city where a couple of criminals reconcile him and attack them both. Rogue touches the leader of them and discovers Gambit's foster father is being hold in an old house near the swamp. They go there and Rogue accidentally touches Gambit and learns he is using her to get there. Gambit decided to go alone but Rogue comes back to help him and rescue his father and take on the Rippers. Wolverine and the rest of the X-men arrive and take Rogue with them while Gambit decides to quit that lifestyle for good.
Kitty is saved from a rockslide by a mutant girl named Danielle Moonstar. Danielle quickly joins the institute, but immediately causes trouble during a training session when she causes the nightmares of Jean, Kurt, and Kitty to come true. That night, Logan, Professor X, and Storm also have powerful nightmares, worrying Kitty that her new friend will be expelled from the institute. When Kitty wakes up the next morning, Danielle isn't there -- and when she asks, nobody has even heard of her. Kitty is determined to find Danielle Moonstar, and follows a path of strange messages that only she is receiving to her location.
When a new sphere appears in Egypt, Professor X wants to try to communicate with Apocalypse, taking Storm with him. With Cerebro technology, the rest of the group watches as Apocalypse telepathically communicates his plan to awaken the dormant X gene in all humans, a process which will kill most 'normal' humans. Xavier tells Apocalypse that this isn't necessary, which angers Apocalypse. Storm comes to his defense, but instead sends them both away in the same way Magneto was. The X-Men are mortified, and are soon joined by Nick Furry who announces the restart of the Sentinel program. Apocalypse is confronted by three sentinels at the Sphynx, which act as decoys while more sentinels are sent to use their superior technology to disable the three spheres. Apocalypse defeats the sentinels, but sends out four horsemen under his control to protect them - Magneto in Mexico, Storm in China, Xavier in Egypt, and Mystique at the Sphynx. The X-Men split into four groups to fight the horsemen aroun
The four teams fight a losing battle against their horsemen, until Apocalypse moves his plan to the next level. The tops of the pyramids come off and line the Earth's atmosphere, connected to each other by some sort of energy. Pressed for time, the teams become desperate. The Brotherhood joins the team in Mexico to fight Magneto, and Jean amplifies her power with Cerebro to battle Xavier psychically. Apocalypse lies down in his original resting place, and the evolution of humankind begins. But in the last moments of the battle, Rogue shows up with Leech, and she takes his power and negates Apocalypse's power, ending the evolution before any harm is done. Apocalypse is shut into his machine and sent to another time period, and the horsemen fall out of their trances. Rogue and Kurt give Mystique the cold shoulder, and the episode ends with Xavier deeply disturbed after seeing glimpses into the future of the X-Men, and seeing Jean become the Phoenix, among other changes.