Dr. Shinji Mafune appeared in Terror of Mechagodzilla as a marine biologist formerly employed by the Ocean Exploitation Institute, noted for his discovery of the undersea dinosaur Titanosaurus. The death of his wife, coupled with him losing his job at the Institute because of his controversial mind-control experiments with sea life, drove Mafune insane and made him swear revenge against humanity.
He joined forces with the second coming of the Black Hole aliens, owing them everything after their surgeons had saved the life of his daughter Katsura by turning her into a cyborg. He gave them Titanosaurus to use against Godzilla, and later his mansion on Manazura Island became their new base of operations after the original was destroyed after the shenanigans of Interpol agent Jiro Murakoshi.
Mafune was betrayed by the aliens, as Mugaru and Tsuda put Mechagodzilla's controls into Katsura, making her even less human than before, causing Mafune to rethink his actions. When Interpol agents attacked the mansion, Mafune turned against his former allies and attempted to tackle Mugaru, however the alien leader used him as a human shield and the scientist was accidentally shot and killed by Murakoshi.