Mr. Fuji appears as a kind-hearted elderly man in Lavender Town, operating the Lavender Volunteer Pokémon House to care for abandoned and orphaned Pokémon. This includes a Cubone orphaned when Team Rocket killed its Marowak mother, alongside others like a Nidorino and Psyduck.

His past reveals a transformation. Previously known as Dr. Fuji, he was a scientist affiliated with Team Rocket on Cinnabar Island. He played a central role in the unethical creation of Mewtwo through genetic experimentation on Mew, documented in diaries within the Pokémon Mansion. After the laboratory's destruction and Mewtwo's escape, Dr. Fuji, burdened by remorse, abandoned science. He relocated to Lavender Town, adopted the name Mr. Fuji, and dedicated himself to atoning for his past by sheltering suffering Pokémon. He rarely discussed this history, fostering an enigmatic presence.

His compassion surfaced during Team Rocket's crisis at Pokémon Tower. He confronted them over Pokémon abuse and was taken hostage at Marowak's grave, requiring rescue by protagonist Red. Afterward, he gifted Red the Poké Flute to awaken Snorlax blocking routes.

Connections to his past as Dr. Fuji emerge through evidence. A portrait in Cinnabar Gym shows him with Gym Leader Blaine, confirming their association. Documents in the burnt Pokémon Mansion detailing Mewtwo's creation are later attributed to "Professor Fuji" in supplementary lore, reinforcing his dual identity. In *Pokémon Origins*, during Mewtwo's rampage, he provided Red a Mega Stone enabling Charizard's Mega Evolution to subdue Mewtwo, symbolizing his indirect attempt to rectify his past work.

Lavender Town residents describe him as profoundly kind and selfless yet shy and reserved about his origins. Rumors suggest Cinnabar Island roots, but he declines interviews, maintaining a quiet life focused on rehabilitation.