A plutonium tanker run aground on a mysterious moving atoll. Yonemori, a naval officer escorting the tanker, is shaken by the disaster that was narrowly avoided, and joins the investigative team to track down the atoll and ascertain its true nature. Meanwhile, Nagamine, an ornithologist, is summoned to investigate the destruction of a scientific establishment on Himigami Island. The scientists stationed there reported a giant bird, although she is doubtful any bird could have caused the devastation. Nagamine discovers that three new specimens of a reptilian, flying creatures on the island are responsible. Furthermore, these creatures are man-eaters, and a threat to other islanders’ safety. Nagamine is recruited by the Japanese government to capture the creatures.

Yonemori’s team finds the atoll, and inspects an ancient plaque embedded in the surface. The atoll comes alive and sheds its rocky exterior, and Yonemori glimpses a giant turtle monster emerging from the debris. Nagamine arranges to lure the flying creatures to Fukuoka baseball stadium, so they can trap them with the closing ceiling. Everything goes according to plan until the turtle monster appears and attacks the stadium. The flying creatures escape, and the turtle monster flies away to pursue them. Yonemori uses a translation of the ancient plaque to identify the turtle monster as “Gamera” and the flying creatures as “Gyaos.” The government makes Gamera the primary target for the self defense force, even though Gyaos is actively hunting down and eating people.

In subsequent encounters with Gamera and the SDF, only one Gyaos survives. This Gyaos grows to enormous size and attacks a commuter train in Tokyo. The military repents and makes Gyaos’ destruction top priority. Their initial assault backfires and destroys Tokyo Tower. Gyaos takes roost in the remains of the tower and starts laying eggs. Gamera reappears and destroys the nest, and a prolonged fight begins in the air over Tokyo and on the ground. The battle culminates in a showdown in an oil refinery, where Gamera decapitates Gyaos with a well-placed fireball. Gamera returns to the ocean.