Three years have passed since Gamera defeated Legion and the world is once again plagued by Gyaos, which have evolved into Hyper Gyaos. Mayumi Nagamine, noted ornithologist, returns to aid the Japanese government in addressing this threat. A graveyard of Gamera fossils is found at the bottom of the sea. Shadowy government agents, occultist Miss Asakura and Kurata Shinya, are meanwhile working to a different agenda, with Asakura believing Gamera to be an evil spirit.