After an unfortunate and mysterious accident, Professor Charles Xavier and Jean Grey mysteriously vanish in an explosion outside the Institute. One year later, Wolverine returns for Beast's help when a family gets arrested for helping him.
Wolverine and The Beast attempt to re-unify the X-Men.
With the aid of of an unlikely ally, Emma Frost, Wolverine and the X-Men must find Professor Xavier and bring him back to the newly rebuilt Institute.
After receiving a telepathic message from the future from Professor Xavier, Wolverine and the X-men must journey to Africa to find Storm, who apparently some time in the future killed and destroyed every single living been in said continent.
Magma is being chased by the Mutant Control Unit. In the middle of a road she turns to a burning being and the cars suddenly stop around her. Wolverine rescues Magma from the Mutant Control Unit and uses an inhibitor collar built by Forge to help control her powers. Wolverine asks for the collar back, she is reluctant to take it off, but finally takes it off. Meanwhile, Dr. Sybil Zane hires Gambit to steal that collar from the X-Men for Senator Kelly and it is up to Wolverine to get it back. Gambit attacks Wolverine in his laboratory with fire cards, he admits to Wolverine that he has been hired for cash, but Wolverine sets his money on fire and offers him double the amount, if he helps discovering whom he is working for. In the end Gambit and Wolverine manage to get back the collar.
Nightcrawler sneaks aboard a cargo ship on the way to Genosha when he hears that mutants are being mistreated.
Nick Fury of S.H.I.E.L.D. taps Wolverine to stop the Hulk who apears to be terrorizing the Canadian Rockies.
Xavier tells the X-Men that they must protect the Bortherhood and bring a mutant to the MRD
In the future, Xavier is captured by Centinals and Cerebro is stolen; while in the present, Wolverine and the X-Men investigate something Logan saw when taking back the inhibitor collar from Trask.
Nightcrawler arrives at Genosha, where everything seems too good to be true.
Haunted by a fragmented memory, Wolverine heads to Canada to try to piece it together.
The brooding, heart-sick Scott Summers is so desperate to find the missing Jean Grey that when he spots Harpoon, an old enemy of the X-Men on the street, he goes berserk. Harpoon was an agent of the vile mutant geneticist known as Sinister—someone that Scott believes could be responsible for Jean's abduction. Now, based on nothing but his own suspicions, the out-of-control Cyclops forces his way up Sinister's ladder of command, one rung at a time. But the closer Cyclops gets to Sinister himself, the more danger he's in. Wolverine and the X-Men race to find him, but Cyclops is walking into a carefully laid trap. And it could already be too late.
Rogue tried to tell Logan what Magneto and the Brotherhood were up to but he would listen. It wasn't until after they attacked that he believed her. Now, pitted in battle against the Brotherhood, the X-Men are kept busy while Magneto initiates a precision strike against MRD facilities across the country. The humans are under siege, and Magneto's coup de grace will put more than just Kelly's troops in danger unless the X-Men can find a way to stop it.
When Logan gets an anonymous call that Christy Nord is in danger, he leaps into action. She¹s the grown daughter of a man Logan had abducted back when he was a Weapon X Agent, and now he feels responsible. When Logan checks on her, he finds out Weapon X has already taken her. With help from a from a surprising ally, Mystique, the two of them set out to infiltrate Weapon X, and bring Christy back safely. But the more time Logan spends with Mystique, the more he realizes she has her own agenda to pursue.
NIghtcrawler and Wander are taken to a mysterious dimension for a strange creatures entertainment: fighting.
WOlverine, Kitty and Forge try to find info on "Master Mold" while in the future, Xavier and the renegade mutants are chased by Centinals with startlingly familiar atributes.
The Silver Samurai captures all the X-men in order to get a rematch against Wolverine for a fight lost in the past
The sentinals are activated forcing the X-me and Brotherhood to work together to stop them.
Warren aka Angel takes it upon himself to rescue mutants who are being captured by the MRD. His actions take interest of Sinister.
When Scott starts seeing Jean everywhere, Emma suggests she blocks those memories of her. This has Scott reminiscing how he came to the Institute and how he met Jean.
While the X-men try to figure the next steps to stop the war, the future renegade mutants figure out a crucial past event that may help.
Wolverine and NIghtcrawler gead to Genosha to try to prevent Magneto's helmet from being stolen
After Jean uses her powers, Scott and Emma head to bring her home, before Sinister gets to her.
Jean is kidnapped by a group of psychics who want to unleash the Pheonix. Magneto sets up Mystique to pretend to be Sen. Kelly, and has her launch an attack on Genosha
In the future, just when things start to get dicey, a familiar face comes to the rescue. In the present, Scott and Emma try to rescue Jean while Magneto counters the sentinal attack.
Xavier and the renegades go against Master Mold in the future, while it's a race against time to stop the Phoenix from destroying the world in the present.