Mafune is depicted as a brilliant, but tragically insane scientist blinded by his thirst for revenge on the civilization that shunned him.
Many years ago, Mafune was once a brilliant and respected scientist at a prestigious oceanographic center in Japan. Many were intrigued by his plan to create vast undersea ranches. However, his colleagues soon started to question his ethics when he proposed a means to mentally control forms of sea life. During the course of his experiments, Mafune claimed to have discovered a giant dinosaur living under the sea that he named Titanosaurus, which he also claimed to have control over. This claim caused many of Mafune's colleagues to dismiss him as insane and cost him his career as a scientist. Embittered, Mafune retreated to seclusion at his home at Manazuru and continued his experiments with his daughter Katsura, planning to one day take revenge on humanity. Katsura was seriously injured in an accident at Mafune's lab and was saved by a mysterious group of men, who actually turned her into a cyborg. Many years later, a representative of this group of men returned to Mafune and revealed himself as a member of the Black Hole Aliens. The aliens promised Mafune and his daughter a prosperous life in their new utopian world order in exchange for the assistance of Titanosaurus in their invasion. Gradually, Mafune came to realize that the aliens were exploiting his daughter as a means to control Mechagodzilla and became deeply regretful for causing her fate. When Interpol raided Mafune's lab, the alien leader Mugal used him as a human shield, causing him to be fatally shot in the chest.
- Dr. Mafune was the last role in a Godzilla film for Akihiko Hirata, who had previously played several characters in the Showa era, including Daisuke Serizawa.