After a mysterious explosion at the Xavier mansion, and the resulting disappearances of Professor Xavier and Jean Grey, the distraught X-Men disband. But soon, Wolverine, Storm. Beast and the others find themselves together again to battle the increasingly powerful Mutant Response Division, and to prevent a catastrophic future that Xavier has warned must never come to pass.
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Foresight (3) 01x26
The X-Men, MRD and S.H.I.E.L.D. fight against Magneto's Sentinels. Meanwhile, the Inner Circle reveals to Scott that Emma and the Stepford Cuckoos were the ones responsible for setting in motion the events that would lead to the destruction of the mansion, Xavier's twenty-year coma and the eventual extraction of the Phoenix Force from Jean's mind and body. Upon the successful transmission of the Phoenix Force from Jean and into the bodies of all five Stepford Cuckoos, the possessed girls are then instructed by Sebastian Shaw to destroy the Sentinels, the X-Men and Genosha, an action which was completely unknown to Emma whose initial plan was to both locate and destroy the cosmic entity before it could reach maturity and bring forth unparalleled global destruction. In the wake of her regretable actions, Emma attempts to redeem herself in the eyes of the X-Men, especially Scott, by ultimately sacrificing herself in order to successfully destroy the Phoenix Force entity. In the aftermath of the carnage, Magneto is banished from Genosha for his radical actions while his eldest daughter, Wanda, assumes authority over the destroyed island and its inhabitants, alongside her sister Lorna, in an attempt to rebuild from the demolished remains of her father's mistakes. From the future, Xavier informs the X-Men that their mission was a success and that the bleak, sentinel-run world has now been avoided. However, there is a new and far more formidable future that has taken its place: the Age of Apocalypse.
Foresight (2) 01x25
Emma discovers the Hellfire Club's true motivation for using the Phoenix Force, and fights to free Jean alongside Cyclops. In Genosha, Magneto's plan comes to fruition as Sentinels ravage the island, providing just cause for Magneto's war against humanity. Accordingly, Magneto reprograms the Sentinels to attack humans. In the future Professor X and the future X-Men are freed by Wolverine, and together they take up a fight against Master Mold. Trivia: Magneto's reprogramming of the Sentinels is very reminiscent of a similar event in Ultimate X-Men, whereby a massive fleet of the Sentinels were sent to Genosha, but Magneto reprogrammed them, and sent them to attack Washington, D.C.
Foresight (1) 01x24
Suspecting Emma's hand in Jean's abduction, Wolverine places her in a holding cell. Emma is later freed by Cyclops, who trusts her to find Jean. Apparently, the Hellfire Club had become aware that the Phoenix Force had possessed Jean and supposedly wants to extract the divine Phoenix Force from her mind and use its infinite and limitless power and strength for their own ends. Meanwhile, Magneto hatches a plot against the human race, having replaced Senator Kelly with Mystique to start an attack on Genosha. In the future, the Professor is apprehended by Sentinels, who have replicated Cerebro to find all mutants in the world.
Shades of Grey 01x23
An amnesic Jean uses her incredibly strong and powerful telepathic and telekinetic abilities while at the hospital, which allows Emma to locate her using Cerebro. Emma and Scott go to the hospital and attempt to take Jean back to the mansion when Archangel intercepts Scott and Jean and takes them to Mr. Sinister where he extracts their genetic codes, stating that combined they will create the very strongest and most powerful force in the world. Before his men can dispose of Scott and Jean, the X-Men arrive and save them. Later, Emma appears to double-cross the X-Men and the Hellfire Club arrives to take an unconscious Jean. Meanwhile, Mister Sinister gives Jean and Scott's DNA to his master, Apocalypse.
Aces & Eights 01x22
Gambit arrives on Genosha under the orders of Senator Kelly to steal Magneto's helmet as a provocation of war, as well as cripple Genosha's resources. Much to the dismay of the Scarlet Witch, Gambit charms Polaris who unknowingly aids him in his task. Wolverine and Nightcrawler head to Genosha to prevent Gambit from stealing Magneto's helmet. Though Gambit seems attracted to Polaris, he leaves her at the end with Magneto's helmet. Polaris gets infuriated and disables Gambit's get away and takes the helmet back. Gambit is then stranded in the ocean. Through the intervention of the X-Men, Magneto and Senator Kelly reach an understanding about their impending war and the dystopian future.
Cyclops and Wolverine inform Professor X of Emma's discovery about the source of the explosion. Fearing that Jean may be responsible for the destruction of Genosha, Professor X and his team of future X-Men try to uncover information on the event from Master Mold's original detention center. The only seen way to get past the Sentinel guards is to send the group's reprogrammed Sentinel "Rover" on a "Kamikaze" attack run. While Bishop has no problem with it, Marrow has developed an incredible bond to Rover and refuses to give him up.
During a battle with Juggernaut, Cyclops is distracted by a vision of Jean and Juggernaut defeats and escapes the X-Men. Emma proposes to erase all memories of Jean from Scott's mind and he accepts. When Emma enters his mind, she looks at all his memories. The truth behind the explosion is revealed to be Jean transforming into the almighty, cosmic Phoenix.
Guardian Angel 01x19
After furiously snapping at his father on the development of a so-called "cure" for mutants, Angel's wings are severely damaged at the hands of the MRD and are ordered to be cut off. However, Mr. Sinister then makes him a proposal that will change his life forever, transforming Angel into Archangel and with even stronger angelic wings.
The MRD starts hunting mutants without warning, forcing the X-Men to strike back. Angel joins the X-Men and tries to destroy the artificial intelligence/multi-agent system, Mastermold, accompanied by the Brotherhood who were betrayed by Magneto. However, the dystopian future still exists and Mastermold had transferred itself to a damaged Sentinel.
Code of Conduct 01x17
Wolverine comes back to the mansion to discover that the Silver Samurai had captured the X-Men. Having been defeated by Wolverine a few years ago, the Samurai forces Wolverine to fight him to death and regain his honor, in order to officially become a Yakuza clan leader. The odds are stacked against Wolverine as the rules of the duel restrict him from using his claws, and he has long since forgotten how to fight with a sword.