Jean Grey is the Phoenix and is being controlled by an unknown source as Scott Summer (Cyclops) is doing everything he can to either calm her down or have her surface back as a controlled self. Jean decides the best way to save everyone is to destroy herself and implode. The team goes into shambles and the X-Men recede.
Months later professor Xavier learns of something disturbing and contacts Beast, Cyclops, Wolverine, and Storm. Each one of them comes back to the X-Man mansion except Cyclops. The rest of the team assembles to go find him, and find him in the area where Jean last sacrificed herself in. Scott decides he wants nothing to do with the team and everyone returns to the mansion.
Professor X tells the X-Men that he has lost contact with a part of Japan, and Cerebro the master computer that amplifies Xaviers Telepathic abilities is unable to locate a single mutant in Tohoku, Japan even though the area was designated to have a high concentration of mutants. It is up to the X-Men to investigate.
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