Three years have passed since
Gamera defeated the Legion, and the world is once again plagued by the Gyaos, which have now evolved into Hyper Gyaos. Mayumi Nagamine, noted ornithologist, returns to aid the Japanese government in addressing this threat. At the bottom of the
Pacific Ocean, a graveyard of Gamera fossils is found. Meanwhile, two government agents, occultist Mito Asakura and Kurata Shinya, are working with a different agenda, with Asakura believing Gamera to be an evil spirit. At
Shibuya, Gamera fights and kills a pair of attacking Hyper Gyaos with little regard for humans; with up to 20,000 people killed in the crossfire, the Japanese government orders Gamera's destruction. Meanwhile, a teenage girl named Ayana Hirasaka, whose parents were inadvertently killed by Gamera during his previous battle with Super Gyaos in 1995, discovers a stone egg sealed within the temple of Asuka. The egg hatches a tentacled mutant creature known as the “Ryu-sei-cho”, which Ayana names "Iris" after her deceased pet cat. Ayana forms a link with Iris through an
orichalcum magatama amulet, and plans to raise Iris to take vengeance against Gamera. However, as Iris grows larger, he attempts to absorb her. Ayana's classmate, Tatsunari Moribe, manages to free her from Iris's
cocoon with a sacred dagger, but Iris later massacres half of Asuka's populace, subsequently growing into his adult form. The
JGSDF attempts to destroy Iris, but fails after Iris flies toward
Kyoto, where Ayana has been taken by Asakura and Kurata, who plan to use Ayana to summon Iris. En route, Iris attempts to kill two
JASDF F-15J Eagle pilots tasked with intercepting the monster, but Gamera comes to the rescue and engages Iris in battle. Gamera is struck and slowed down by
air-to-air missiles fired by the F-15s, inadvertently allowing Iris to escape. At
Kyoto Station, Nagamine and Asagi Kusanagi, a teenager once psychically linked with Gamera, attempt to extract Ayana out of Kyoto, when a typhoon hits the city. Kurata speculates that Gamera was engineered as humanity's guardian, and can be charged with humanity's collective "mana", and theorizes Iris was similarly created to defeat Gamera so the Gyaos could wipe out the human race. While rejecting Kurata's misanthropy, Nagamine and Asagi think his theory explains how Gamera got the energy he used to defeat Legion. Iris makes his way to Kyoto Station, continuing his duel with Gamera. Iris impales Gamera with one of his tentacles and destroys the station, killing Asakura and Kurata. Moribe briefly distracts Iris with the dagger, but Iris ultimately absorbs Ayana. From within Iris's body, Ayana experiences his memories, realizing her hatred and anger motivated him. As she has this epiphany, Gamera plunges his hand into Iris' chest, pulling Ayana free and robbing Iris of his human link. As Asagi rescues Nagamine, Iris impales Gamera's hand and begins processing his DNA. Gamera blasts off his injured arm, absorbing Iris's fireballs and forming a fiery plasma fist, which he drives into Iris, destroying him. Setting a comatose Ayana down, Gamera awakens her with a roar after Nagamine and Asagi fail to revive her, leaving her mystified by Gamera's forgiveness. As a swarm of Hyper Gyaos begins to converge on Japan, military leaders finally realize that Gamera is on the side of humanity and pledge to fight the swarm alongside him. Asagi states that despite no longer sharing a psychic link with Gamera, she knows he will fight to the end. As the swarm approaches, Gamera defiantly roars at the center of Kyoto. ==Cast==