After an unexplained and unexpected explosion of the X-Mansion, Professor Charles Xavier and Jean Grey are missing. The X-Men disband and Scott begins to suffer from depression. One year later, the Mutant Response Division (or MRD for short) is imprisoning mutants. Emma Frost is able to locate a… More comatose Charles on Genosha in the care of Magneto. Professor X telepathically orders Wolverine to lead the X-Men and set out to save the world from The Sentinel Project and prevent the Brotherhood of Mutants from taking over the world before the future ends up dominated by Sentinels.
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 centre. Unfortunately, Marrow's attachment to a reprogrammed Sentinel named Rover complicates things.
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...
Now a member of the X-Men, Angel's wings are severely damaged at the hands of the MRD and have to be cut off. Mr. Sinister then makes him a proposal that will change his life.
The MRD starts hunting mutants using Sentinels, forcing the X-Men to strike back. Angel joins the X-Men and tries to destroy Master Mold accompanied by the Brotherhood who were betrayed by Magneto. However, the dystopian future still exists and Master Mold had transferred itself to a damaged Sentinel.
To regain his honor, Silver Samurai captures the X-Men and attacks Wolverine.