A ship carrying plutonium collides with a floating atoll off the eastern coast of the Philippines, one of many incidents occurring throughout the area. As the anomalous formation approaches Japan, a team of scientists led by Naoya Kusanagi (Akira Onodera) discover orihalcum amulets and a stone slab covered in Etrurian runes on the atoll. During the investigation, the atoll suddenly quakes, destroying the slab and throwing the scientists into the ocean. One member of the team, Marine Officer Yoshinari Yonemori (Tsuyoshi Ihara), sees the eye and tusk of a giant turtle.
Meanwhile, ornithologist Mayumi Nagamine (Shinobu Nakayama) investigates a village in the Goto Archipelago reportedly attacked by a "giant bird." While Nagamine is initially skeptical of the claims, she is horrified upon discovering human remains in a giant bird pellet. Exploring the nearby forest, her team encounters and then successfully prevents a bird-like creature from attacking another village. To prevent further attacks, Nagamine agrees to aid the government in capturing the giant bird. The creature is lured to the Fukuoka Dome baseball stadium,where she is successfully captured.she escapes to the harbor, where she is growled at by the giant turtle encountered by Yonemori and the scientists. The bird escapes before the turtle reaches the stadium.
After translating the runes, Kusangi explains to Yonemori and his daughter Asagi (Ayako Fujitani) that the giant turtle is called Gamera and the bird is Gyaos. When Asagi touches one of the stone amulets, she inadvertently forms a spiritual bond with Gamera. Kusanagi also tries to convince the government that Gyaos is the threat, but they remain focused on Gamera due to the destruction he caused.
Now working together to investigate the creatures, Kusanagi, Yonemori, and Nagamine witness another Gyaos attack at the Kiso Mountain Range. Nagamine and Yonemori are nearly killed trying to rescue a child, but Gamera arrives in time to save them and attempt to kill Gyaos, who, however, escapes. Meanwhile, Asagi discovers that she suffers the same wounds and fatigue as Gamera due to their shared bond. At Mount Fuji, she witnesses a military strike against Gamera. The attack attracts Gyaos to the scene, where she grievously wounds Gamera and forces the turtle to retreat into the ocean. Simultaneously, Asagi suffers a similar wound and passes out from the pain. Kusanagi visits his daughter at the hospital where Asagi falls into a coma after saying that she and Gamera must rest.
After consulting with a biologist, Nagamine and Yonemori learn that Gyaos is genetically engineered and reproduces asexually. They speculate on the origins and purpose of Gyaos and Gamera. Nagamine suggests that Gyaos was awakened by rampant pollution and Gamera was created to combat Gyaos. They approach Kusanagi with this information, explaining that the incident at Mount Fuji shows that Asagi is spiritually linked with Gamera. Kusanagi dismisses these claims until he witnesses the amulet's power himself.
With Gamera recovering in the ocean,Gyaos grows unchecked, becoming Super Gyaos. The creature attacks Tokyo, causing many civilian casualties and prompting the government to focus on Gyaos instead of Gamera. Attempts to kill Gyaos end in failure and she builds a nest in the ruins of Tokyo Tower.
Upon awakening from her sleep, Asagi warns the others that Gamera has recovered and will attack Gyaos. Gamera catches Gyaos by surprise, destroying her nest and eggs. A massive air battle ensues and Asagi, Kusanagi, Nagamine, and Yonemori follow closely in a helicopter. Initially, Gyaos overpowers Gamera, but Asagi uses her spiritual energy to revive Gamera, who kills Gyaos. Gamera then releases Asagi from their bond and returns to the sea.Gamera as himself
Gyaos as herself
Tsuyoshi Ihara as Yoshinari Yonemori
Akira Onodera as Naoya Kusanagi
Shinobu Nakayama as Mayumi Nagamine, a gifted ornithologist who is also a friend of Asagi's.
Ayako Fujitani as Asagi Kusanagi, a young girl who forms a spiritual bond with Gamera after she received an ancient pendant found on Gamera's shell by her father.
Yukijirō Hotaru as Inspector Osako
Hatsunori Hasegawa as Colonel Satake
Hirotaro Honda as Mr. Saito
Akira Kubo as Captain of the Kairyumaru
Kôjirô Hongô as Captain of the Nojima
Peter H. Gilmore of MonsterZero.us said, "All in all, this is a vibrant and energetic film. The monster battles are full of physical grappling as well as energy weapon exchanges, and the excellent suitmation is well augmented by judiciously used CGI." Popcorn Pictures said, "This is just a great, fun kaiju film. ... Gamera finally has a film to rival Godzilla (but he's still second best to the Big G, though) and rid the infamous legacy that has dogged him throughout his motion picture life." David Miller of CULT MOVIES praised the film's special effects, calling the film, "one of the best of all the giant monster films". Steve Biodrowski of CINEMAFANTASIQUE praised the film's "money shot" moments, stating, "supplying the necessary 'oomph' to push this over from being merely diverting to being outright exhilarating". The New York Daily News praised the film's action sequences, stating, "giant monster movie fans seeking a big-screen treat will find it here". Roger Ebert gave the film three stars out of four, saying that, despite its flaws, "Gamera is more fun" than "megabudget solemnity like Air Force One", and that "Gamera is not a good movie, but it is a good moviegoing experience".