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Japan existed in multiple universes.
Tokyo was located in Japan in at least one universe. (COMIC: MechaGiantJunterling)
In Reality Z-25 31-H, Takako Yoshido, later Battle Angel, was born in Yokohama, Japan. Her father was in debt to the Japanese criminal organisation known as the Yakuza, who eventually had him killed before taking his daughter and widow into slavery, training the former as an assassin from the age of twelve. (PROSE: Battle Angel Yoshida Bio)
In one universe, Imperial Japan persisted into the modern age as a warmongering power. By the time the local incarnation of Jenny Everywhere was on the cusp of discovering her powers, they were successfully holding Manchuria and had made advances into Outer Mongolia. (COMIC: The Genesis of Jenny Everywhere)