After nearly half a century of peace, Godzilla is a distant memory for most of Japan. The serenity is broken, though, when a US nuclear submarine is attacked and destroyed: Godzilla is back. Meanwhile, fictional documentary reporter Yuri Tachibana spots a mysterious old man near Mt. Myoko in Niigata who promptly vanishes. That night, the area is attacked by a creature described as "Red Godzilla". The beast turns out to be Baragon. Yuri begins to research and uncovers a book stating that Baragon is one of three guardian beasts along with Mothra and King Ghidorah. The book was written by Hirotoshi Isayama, who it turns out was the mysterious old man near Mt. Myoko. Hirotoshi foretells that the guardian monsters must be awakened to meet the oncoming threat of Godzilla...