Dr. Fuji, a scientist specializing in cloning technology, became consumed by grief after his daughter Amber died in a car accident. He dedicated his research to resurrecting her using remnants of her conscious energy, an obsession that drove his wife away due to ethical objections.

Giovanni, leader of Team Rocket, provided funding and resources for Fuji's experiments on New Island. In exchange, Fuji agreed to develop a genetically enhanced clone of the mythical Pokémon Mew [citation:]. This project yielded multiple fatal failures—cloned Pokémon designated Bulbasaurtwo, Charmandertwo, and Squirtletwo perished—before culminating in Mewtwo's creation.

Alongside Mewtwo's development, Fuji secretly attempted to clone Amber. The resulting Ambertwo existed transiently in a dreamlike state, forming a telepathic bond with the infant Mewtwo before vanishing alongside the other starter clones, shattering Fuji. He then administered an emotion-suppressing serum to Mewtwo, potentially contributing to its instability.

Upon awakening, Mewtwo discovered its artificial origins from Fuji and the scientists. Enraged at being an experiment, it destroyed the New Island laboratory. Fuji perished in the destruction, his final words acknowledging the success of creating "the world's strongest Pokémon."

Fuji's legacy influenced later portrayals of Mr. Fuji in Pokémon games, retroactively linking him to Mewtwo's creation and the Cinnabar Island lab. His character design and narrative role draw inspiration from Dr. Tenma in *Astro Boy*.