Just one year after the Rodans’ sacrifice, Godzilla raids again. An astronaut and a single father named Takegami returns home to his daughter, Sara, in Mt. Fuji. After his space travels, he unknowingly catches a virus within him and slowly his body starts to change. While scientists study Takegami and try to find a cure, Takegami starts going through changes and slowly turns into a gigantic humanoid monster named "M". Sara tries to protect Takegami from the SDF who don't believe in the notion that he turned into a monster and try to shoot him down. In the meantime, Takegami (M) makes an effort to battle the King of the Monsters himself, Godzilla, in order to protect his loving daughter and Japan.