A great duel of supersonic speed. A ship runs aground on a mysterious atoll leading to an investigation by insurance representative Kusanagi, who discovers an ancient bead that he gives to his daughter Asagi. Meanwhile, ornithologist Nagamine investigates reports of a new species of large bird named Gyaos. As the Gyaos begin to attack, an ancient guardian with a bond to Asagi emerges.

As alien invaders plot to conquer the Earth, two Boy Scouts steal a mini-submarine and discover Gamera in their midst. Transported to the alien's spaceship, the Scouts are menaced by the evil inhabitants, including Viras, a squid-like monster that grows to colossal size to battle Gamera.