Everything is changing for the X-Men. The team is disbanded, the world hates them now more than ever, new threats loom on the horizon. What a time to pick for the return of Hank McCoy...
The issue opens in the Triskelion. Mr. Sinister has been on suicide watch for months, and the guards standing over him marvel at his corpse, his shirt hanging out of his mouth. Despite a lack of access to weapons or other instruments, Mr. Sinister is dead due to suffocation. At the same time a guard walks down the hall with a lunch delivery for one of S.H.I.E.L.D.'s most dangerous prisoners--the mutant terrorist Magneto. As the guard enters Magneto's plastic cell with a lunch delivery, he reveals to its occupant his true form; Mastermind has been sent by the real Magneto to relieve Mystique of her post. With him is Stacy, a mutant that shall keep him company during his stay as Magneto.
Meanwhile, the remaining former students of Xavier are learning to cope with their new roles at the Xavier School for Gifted Children. After helping an upset student cope with his gifts and grizzly appearance, Scott and Jean discuss adding new personnel to the staff (Moira MacTaggart). At Emma Frost's Academy of Tomorrow Emma Frost introduces her boyfriend Shinobi Shaw to her students. Shinobi receives a call from Gerald, the member of the Shi'ar religion that is acting as Lilandra's liaison at the school and possible double agent of the Hellfire club gives Shinobi a call which he ignores.
After searching the sewers, Nightcrawler may have finally found somewhere where he can feel welcome. Nightcrawler locates a lone disfigured mutant who guides him to the underground lair of the Morlocks.
Back at the Science Lab Level of the Triskelion, Nick Fury greets an unhappy "employee". Beast is alive, and has successfully removed his blue fur. When Beast was believed to be dead he was actually resurrected at a nearby hospital. Fury took the opportunity to employ the bright student of Xavier's with S.H.I.E.L.D.. Until his recent "death", Xavier was leading Hank McCoy to believe that he was still keeping in touch with his family and friends to keep him compliant. Because he was no longer under control, Beast has realized what is going on and is not happy. He wants to leave, but Nick Fury and his sense of duty keep him tethered to the lab. Beast is close to a breakthrough in his search for a cure for the Legacy Virus.
Finally, the Sentinels are here, and they are targeting rogue mutants with extreme prejudice, Storm is having nightmares of a Shadow King, and Bishop has recruited Storm to help him assemble a new team of X-Men. With everything that appears to be just around the corner, it appears that the world still needs costumed mutants for its survival.