After Godzilla's first attack in 1954, Japan enjoyed a period of peace for 50 years. In 2004, an American nuclear submarine sunks. During the investigation of the site a Japanese research submarine, Satsuma, spots glowing blue fins in the background... Although the idea that Godzilla has reappeared is taken with some skepticism, the Japanese Self-Defense Force (JSDF) is confident that they will be able to defeat the monster with modern conventional weaponry not available fifty years before. A mysterious old prophet concludes that this Godzilla is invincible, driven by the rage of the souls of all those lost to Japanese aggression during World War II. In order to protect Japan from Godzilla, the old prophet awakens the ancient Yamato monsters, Baragon, Mothra, and King Ghidorah.