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.
A pair of Gyaos glide across Tokyo's Shibuya district, but are destroyed by Gamera at the cost of twenty thousand human lives, causing the Japanese government to order Gamera's immediate destruction. Meanwhile, a young girl named Ayana, whose parents were inadvertently killed by Gamera during his previous battle with Gyaos in 1995, discovers a stone egg sealed within her village temple. The egg hatches a small tentacled creature, whom the girl names "Iris" after her dead pet cat. Iris forms a link with Ayana through an orichalcum pendant, and becomes the focus of Ayana's quest for revenge as she seeks to raise her own monster and take vengeance against Gamera. Iris however attempts to absorb Ayana in the process of his growth. The girl's classmate manages to free her from Iris' cocoon, but it leaves its lair and kills half of the village's populace, later growing into its adult form. The military attempts to destroy it, but fails.
Iris flies toward the city of Kyoto, where Ayana has been taken by Asakura and Kurata, with Asakura deliberately trying to use the girl to summon Iris. Iris is intercepted in mid-flight by Gamera, and the two engage in an aerial battle, but the Japanese army intervenes and knocks Gamera out of the sky with a tactical missile strike. Nagamine and Asagi, the girl once psychically linked with Gamera, retrieve Ayana and attempt unsuccessfully to get her out of Kyoto. Kurata expresses a belief that Iris had been deliberately created to defeat Gamera so that the Gyaos could wipe out modern humanity.
The two monsters meet and continue their fight, but Iris easily gains the upper hand, impaling Gamera and leaving it for dead. Iris then makes its way to the train station and absorbs Ayana, killing Asakura and Kurata in the process. From within Iris' body, Ayana experiences the creature's memories and realises that her hatred and bitterness motivated it. Just as she has her epiphany, Gamera plunges its hand deep into Iris' chest and wrenches the girl free, robbing Iris of its human merge. Miss Nagamine and Asagi, trapped within the train station's wreckage, watch helplessly as Iris impales Gamera's hand and begins to syphon its blood, creating fireballs with its tentacles. Gamera blasts off its injured hand, and absorbs Iris's fireballs, forming a fiery plasma fist, which it drives into Iris' wounded chest.
Iris explodes, blowing the roof off the crumbling train station. The comatose Ayana still clutched in its fist, Gamera sets the girl down where Nagamine and Asagi are hiding. The women are unable to revive her, but Gamera lets out a roar and Ayana awakens. Gamera leaves the girl wondering why it would save her life after all she had done. A swarm of Gyaos, thousands strong, begins to descend on Japan intent on destroying their greatest foe once and for all, while Gamera lets out a final roar of defiance as it stands its ground in the center of a blazing city.Shinobu Nakayama as Mayumi Nagamine – One of the main characters of the series. Mayumi is a scientist who is intrigued by Gamera, and forms a partnership with Asagi due to the latter's past experiences with the monster.
Ai Maeda as Ayana Hirasaka – Ayana is a tormented young girl whose parents were unintentionally killed by Gamera's previous feud with Gyaos. She forms a bond with Iris and her rage fuels the creature's appetite for destruction.
Ayako Fujitani as Asagi Kusanagi - Asagi is Gamera's former human companion, who sacrificed their bond during his fight with Legion three years earlier.
Senri Yamasaki as Mito Asakura - A sadistic woman who believes that Gamera is an evil spirit bent on destruction and that Iris is the key to his downfall.
Toru Tezuka as Shinya Kurata - A mysterious man who claims to be a descendant of the advanced civilization that created Gamera and Gyaos.
Takasaki Nayami as GF Colonel Takoshi - The colonel of the Japanese Self-Defense Force.
Hakosaki Sato as GF General
Kenji Soto as Dr. Sato
Yukijirō Hotaru as Inspector Osako
Masahiko Tsugawa as Commander in Chief of the Air Defence Command (Lieutenant General)
Hirofumi Fukuzawa as Gamera - The movie's titular kaiju and the Guardian of the Universe, Gamera is a giant, fireball-breathing turtle and an ancient biological constructed monster created to destroy the Gyaos, a race of vampiric bird-like creatures.
Akira Ohashi as Iris - The film's main kaiju antagonist, Iris is a creature that must feed on bodily fluids to survive and forms a spiritual bond with Ayana, using her hatred for Gamera to feed its strength. It is Gamera's ultimate foe.
Kei Horie as Shigeki Hinohara - Ayana's Cousin
Aki Maeda as Young Ayana
Yukie Nakama as Female Camper
Many members of the crew who worked on Gamera 3: The Revenge of Iris had previous work in the Gamera film series. Director Shusuke Kaneko directed both Gamera: Guardian of the Universe (1995) and Gamera 2: Attack of Legion (1996). Gamera 3 marks the first Gamera film that Kaneko had screenwriting credits on as he co-wrote the film with Kazunori Ito who had previously written the previous two 1990s Gamera films. The music composer Kow Otani and special effects director Shinji Higuchi was also a regular with the series, previously working on both films.
Gamera 3: The Revenge of Iris was released in Japan on March 3, 1999. The film grossed over $15 million on its release. The film had its North American premiere at G-Fest in 1999 and was also shown at the 1999 Toronto Film Festival. The film did not have a wide release in North America, and was released direct-to-video on DVD on June 10, 2003 by A.D.V. Films. The film was released on Blu-ray by Mill Creek Entertainment on September 27, 2011.
Gamera 3: The Revenge of Iris was followed up by Gamera the Brave directed by Ryuta Tasaki in 2006. The film's plot ignores the events of the three films directed by Kaneko.
In Japan, Gamera 3: The Revenge of Iris won the award for Best Sound Recording at the 54th Mainichi Film Concours ceremony.
Western reviewers praised the film as one of the best in the Gamera series commenting on the special effects in the film. Variety stated the film was "somewhat more elaborate" and "grittier and hipper" than Gamera: Guardian of the Universe (1995) and Gamera 2: Attack of Legion (1996) as well stating that the monster Gamera appeared "more threatening". Variety also described the special effects in the film as "good by model/miniature/animated standards" but felt that were not up to the standards of American special effects. The San Francisco Chronicle felt the film's plot was similar to an episode of The X-Files and praised the special effects in the film opining that "The special effects are terrific, although the monsters still look like guys in rubber suits. Fans of the genre wouldn't have it any other way." Film critic Tom Mes referred to the film as the best Gamera film to date, opining that the film "delivers everything a movie about huge, fighting, city-stomping monsters should have: excitement, slam-bang action sequences, beautifully designed creatures, and yes, even stunning special effects" Time felt that the film was stronger than Gamera 2: Attack of Legion, stating the film is stronger "because it has much less Gamera; there's only so much character richness, let alone fun, to be found in shell, teeth, eyes, claws, scales, etc. But the movie has thrills for those who need 'em. Toward the end, a young scientist faces Iris and his doom and, a moment before he dies, screams like a cheerleader at his own immolation: "Oh boy, is this scary? Yes!" I second that notion."