When a mutant high school student named Hisako Ichiki goes missing in the northern part of Japan, her parents ask Professor Xavier, for his help. Sensing that the case of Hisako's disappearance is of great importance for mutantkind, he gathers together his X-Men. However, the leader of the X-Men, Cyclops, who had lost his lover Jean during battle, refuses to return.
The X-Men, led by Cyclops, travel via Blackbird to Japan. During their search for Hisako, they discover that she is not the first Mutant to have gone missing. As they move ahead with their investigation, they also learn that the local people are extremely prejudiced against Mutants. Their investigation is hampered by the U-Men, a fanatical group of scientists who experiment on unwilling mutants. The X-Men invade the U-Men's hideout and what they discover is truly horrifying.
While searching the U-Men's headquarters, the X-Men find Hisako and Emma Frost, a mutant with the power of telepathy. Cyclops claims that Emma was the principle cause of Jean's death one year earlier. Emma denies this and explains that she was Hisako's instructor and had come to Japan to rescue her but the X-Men distrust her. Just then, they the U-Men's mad scientist, Todd, launches an attack. During this fierce battle, Hisako's powers as a Mutant are awakened.
The X-Men destroy the U-Men's hideout. Emma's body transforms into a diamond-like consistency as she tries to protect Hisako from a laser beam fired by the dying Todd. This is known as "secondary mutation" amongst the Mutants. The X-Men decide to take Emma and Hisako back to the Xavier Institute for examination. During the flight back, the Blackbird is attacked by a strange bat-like creature who shows the dangerous symptoms of Damon-Hall Syndrome, which can attack those with secondary mutations.
Professor Xavier decides to announce Hisako and Emma as members of the X-Men. Cyclops objects to Emma becoming a member as Hisako starts her training as a member of the X-Men. However, the enormity of her powers confuses her. In order to gain the trust of Cyclops, Emma decides to allow Professor Xavier to perform a telepathic examination so that everyone can see her inner thoughts.
All doubts over Emma are put to rest and the X-Men are united again. Professor Xavier senses that there is an enormous force that they do not understand still present in north Japan. Armed with a vaccine to combat Damon-Hall Syndrome, the X-Men return to north Japan. However, as they are flying back, an unknown and very powerful force causes them to lose control of the Blackbird. Forced to execute a crash landing, they are then attacked by the remainder of the U-Men, and a fierce battle ensues.
Having defeated the U-Men, the X-Men arrive at a facility deep in the mountains. The facility is run by a woman named Yui Sasaki, who originally operated it as a school for Mutant children, which was attended by Hisako. Emma, Wolverine and Beast sense that Yui is hiding something. Yui contacts Professor Xavier in New York and tells him the shocking news that he is the father of a child...that no longer exists.
Riko and Kaga, two of Yui's assistants who have come down with Damon-Hall symptoms, attack the facility. Both of them are injected with the vaccine created by Beast. Emma spies an unfamiliar man when she is in her diamond-like state. Emma is dubious about Jun, wondering if he is the man she saw. Meanwhile, Professor X is flying in the Blackbird to visit the X-Men, but never arrives.
It is discovered that Yui had been giving Riko and Kaga a drug which may have unintended side effects. Meanwhile, Emma appears before Jun, who has descended to the underground facility, and discovers that he is, in fact, the leader of the Inner Circle, Mastermind. The X-Men come running, but Wolverine is confused by the illusion that Mastermind projects and attacks Cyclops.
A room at the back of the underground facility contains the source of the enormous power that has been affecting Northern Japan, and Mastermind plans to use this to control the world. A fierce battle ensues between the X-Men and the Four Pillars of the Inner Circle summoned by Mastermind, with the X-Men managing to defeat them, just as Yui reveals a shocking truth. Meanwhile, Professor Xavier is frantically trying to escape from his mysterious prison.
The source of the power that has been harming the Mutants of north Japan is Takeo, the son of Professor Xavier and Yui. Yui had tried everything to conceal his existence and suppress his powers, but, Mastermind had begun manipulating Takeo's powers for his own ends. The enormity of his power is so huge that it is capable of distorting all of reality and Yui's facility is destroyed. Takeo's power increases and the world begins to twist and distort.
Takeo's powers cause strange phenomena to occur in all over the world, putting all of human and mutantkind in danger. The X-Men stage a simultaneous attack on him, but they're no match for him. Professor Xavier, who has finally arrived, meets his son, both in person and on the astral plane, but Takeo puts up fierce resistance and fights back. No longer mortal, do the X-Men have any hope of defeating Takeo before the World is destroyed?