Geneticist Yui Sasaki formerly ran a school for mutants, the Sasaki Institute, similar to the Xavier Institute. After her son (by Xavier) developed uncontrollable powers, she closed the school to concentrate on her research to eliminate mutant powers to help her son. Initially, the result was a serum that caused others to rapidly develop a secondary mutation.
Subsequently, the medication developed by Yui designed to suppress the secondary mutation from manifesting is losing its effect. Her research assistants Riko and Kaga start to deteriorate, and without treatment they will go insane and die. Cyclops confronts Yui about her knowledge of the increase of secondary mutation incidents in Tōhoku. Yui explains that she thus created the suppressant to combat the manifestations. Beast adds that the Daemon Hall syndrome is spreading outside of Tōhoku, and they need to find a way to stop it as Emma has been the only person to survive her secondary mutation. The X-Men then realize that Emma is missing.
Beast remains to keep an eye on Yui while the rest of the X-Men go in search of Emma. Beast tries to contact Xavier to report Yui’s experimentations but is unable to reach him. Xavier finds himself trapped in a dimensional rift over Tōhoku, created by an extremely powerful telepath.
Meanwhile, Emma has followed Jun to the laboratory’s underground vault. She discovered that Sanada Jun, Yui’s research assistant, is Mastermind in disguise, and confronts him. He reveals that the laboratory holds the power with which he could use to rule humanity. Mastermind also confirms that he projected her image to the X-Men so the X-Men would be distrusting of her and not be willing to accept her as a team mate, because she defected from the Inner Circle. Emma refuses Mastermind’s offer to join him and fights him.
The X-Men track Emma underground. They arrive in time to stop Mastermind from killing Emma. But Wolverine is not fooled by Jun’s facade. Mastermind is forced to reveal himself, and controls Wolverine into thinking he is Jean and that the X-Men are the enemy. This turns Wolverine on his own team mates and he attacks the X-Men. They manage to momentarily subdue a mind-controlled Wolverine and Mastermind’s henchmen.
With the X-Men distracted, Jun makes a dash for the vault, only to be stopped by Cyclops. With Jun stunned, Emma uses her telepathy to reveal Jun’s real identity: Mastermind. A furious Cyclops wants to kill Mastermind. Wolverine, having shaken Mastermind’s mind control, reunites with the X-Men just as Mastermind is about to open the vault.