-->"''Gamera will continue to fight...even if he's alone.''"
-->"''He's not alone.''"
-->"''...Gamera.''"
--->~Nagamine, Asagi, and Ayana, respectively, as Gamera walks out into the flaming ruins of Kyoto to face the impending Gyaos swarm.

The finale of the Gamera trilogy *sob*

In 1995, the battle between Gamera and Gyaos left much of Tokyo destroyed, but buildings were not the only casualties in the city. A young girl named Ayana Hirasaka, who had recently had her appendix taken out, could only watch in horror from her family's van as her house, and her parents within, were crushed by Gamera.

In 1996, Gamera fought the Legion, but in order to defeat the Legion, he had to take drastic measures, which broke his connection to Humanity.

Now, in 1999, under the sea, a graveyard of Gamera skeletons has been discovered. Coinciding with this, reports have been surfacing all over the world that tell of flying, man-eating bird-like creatures. The Gyaos have returned, and their attacks are being tracked by Professor Nagamine. By this time, Ayana, who is living in a village in the mountains, has grown into a bitter young woman, and she often thinks about revenge. Ayana soon finds an egg of sorts in a cave, along with a strange bead, reminiscent of the one that Asagi used to have, and when the creature within hatches, she quickly becomes friends with it, and names it after her deceased cat, Irys. Ayana decides to raise Irys to get revenge against Gamera, for killing her parents.

Later that same night, Gamera fights two Gyaos over the Shibuya district of Tokyo, setting the city ablaze and killing hundreds, if not ''thousands'', of innocent people in the process. Seeing this on a news report, Ayana's hatred for Gamera only grows stronger. The JSDF has also put Gamera back onto their enemy list, and are actively hunting him. Meanwhile, Nagamine has made contact with Asagi Kusanagi and her old friend Osako. Asagi reveals to Nagamine her fear that Gamera's ties with her were severed when the bead was destroyed in 1996. Recently receiving a video game, as well as an address of its developer, Nagamine investigates a man named Shinya Kurata, and his partner Mito Asakura, both of whom are involved in some kind of conspiracy.

With the reluctant help of her neighbor Tatsunari Moribe, Ayana raises Irys in secret until it decides to "bond" with her. After Moribe rescues Ayana, Irys goes on a killing spree, sucking the fluids outof almost everyone in the village, save Tatsunari, who managed to hide from the creature. After investigating the village, Nagamine and Osako find Tatsunari and attempt to rescue Ayana, who has been kidnapped from the hospital by Asakura and Kurata. Osako stays with Tatsunari, trying to convince him to rescue Ayana as well. Tatsunari eventually agrees and the pair head off to find Ayana. Meanwhile, Irys has grown since its village massacre, and is now almost as tall as Gamera, if not taller. The JSDF is sent in to deal with the monster, but it quickly defeats them and soon goes off in search of Ayana, who is now in Kyoto.

Flying towards Kyoto, which is being hit by a hurricane, Irys is intercepted by two jets, but before it can eliminate them, Gamera appears, dueling with Irys in midair until the military shoots him [Gamera] down. Irys soon makes landfall in Kyoto, and the city is unrpepared for the monster. Making his way towards the train station where Ayana is at, Irys leaves death and destruction in his wake, but he is soon intercepted again by Gamera. The two monsters soon turn Kyoto into a raging inferno as Irys manages to deflect Gamera's fireballs, forcing the turtle to resort to melee combat. Asagi and Nagamine try to break Ayana's bond with Irys in order to help Gamera, but it does not work. When Asakura takes Ayana's bead, she tries to take control of Irys, but this only gets her killed when Irys impales Gamera and sends him crashing into the station. Kurata is also killed after a large piece of debris falls onto him, while Nagamine is wounded.

Irys once again attempts to bond with Ayana, but Moribe steps in the way. After throwing a ancient dagger (which does jack shit) at Irys, the beast deflects it, and it makes a small cut on Ayana's cheek, knocking her out of her stupor. Realizing her situation, Ayana is helples as Irys knocks Tatsunari out of the way and then absorbs her into his chest. Irys then forces Ayana to relive her memories of when her parents were killed, making her realize that their deaths were an accident when Gamera was fighting the Gyaos. Irys then forces Ayana to watch ''his'' memories of killing the villagers, including most of her family and Moribe's family, in a horrific act of cruelty. Just as Ayana begins to lose all hope, she is pulled out of Irys by none other than Gamera. Irys does not take kindly to this, and impales Gamera's right hand with one of his tentacles, which then begins to drain Gamera's fluids, which allows Irys to steal his powers and create fireballs of his own. Gamera, in a bold attempt to stop Irys, destroys his own arm and hand, before Irys releases the fireballs. Gamera absorbs the fire and creates an ''arm of flame'' that he uses to impale Irys, killing the monster and blowing it up.

Meanwhile, the JSDF has received a report that thousands of Gyaos are converging on Japan. The JSDF decides to switch from fighting Gamera to fighting Gyaos, as only with Gamera's help can they hope to survive. Back in Kyoto, Gamera hands Ayana over to Nagamine and Asagi, who try to revive her, but are unable to do so. Gamera then takes matters into his own hands and revives his former enemy. Moribe has survived, and Ayana tearfully apologizes for her part in Irys's rampage. Gamera departs and everyone watches as the Earth's guardian heads out into the flaming ruins of Koyoto, intent on fighting the Gyaos, even if the battle kills him.

----
!!This film contains examples of the folllowing:

* BattleInTheRain: Gamera's fight with Irys in Kyoto happens while the city is being hammered by a hurricane.
* BolivianArmyEnding: The movie ends with Gamera, who lost an arm in his battle against Irys, heading out to face every Gyaos in the world, with said Gyaos all heading for Japan.
* CallBack: To the Showa films, when Gamera protects a small child from one of the Gyaos during his battle in Shibuya.
* CerebusRetcon: Hey, remember that one building that Gamera smashed in order to get at Gyaos during their final battle? Well, Ayana's parents were in there. Also, remember how the runes of that tablet said, "The last hope, Gamera?" Well, turns out that they really meant the "''last hope''", as Gamera is not only the last defense against the Gyaos, but also the last Gamera, period.
* CerebusSyndrome: This film itself just keeps getting darker and darker, with the Gyaos swarm at the end making things seem almost hopeless.
* CliffHanger: This film, and subsequently the Heisei series, ends this way, with Gamera's ultimate fate left ambigous.
** [[spoiler: WordOfGod says Gamera wins. The film apparently reveals that Gamera is god. Maybe not ''the'' god, but certainly ''a'' god. Director (and co-writer of Gamera 3) Shusuke Kaneko has said that when he was making the Gamera trilogy, he looked around Japanese society and saw that the younger Japanese by and large didn't really believe in anything, spiritually or otherwise. He wished to address this in his Gamera pictures. Gamera resurrects from the flames like the mythical phoenix in the first film. In 2, the sign of the cross forms the "me" character in Gamera's name on the title card and Gamera is "dead" for 3 days before resurrecting. To drive this point home, the English card at the end of the film says "GAMERA 1999: THE ABSOLUTE GUARDIAN OF THE UNIVERSE." Absolute. As in a deity. So in ending the movie this way as a message to the Japanese he was addressing, Kaneko basically says "Yeah, Gamera's gonna win. But we're not gonna show it to you. You have to BELIEVE he's going to win."]]
* CombatTentacles: Irys, which he can use to drain the life out anything and even create and fire sonic beams similar to Gyaos, and even fireballs similar to Gamera, after draining some energy from him.
* DarkerAndEdgier: Definitely darker than any previous Gamera movie, and most Godzilla films for that matter.
* DarkIsNotEvil: Gamera is dark colored, compared to Irys who is shiny and bright, with red and silver coloration.
* {{Deconstruction}}: Gamera 3 being the biggest example in the trilogy. The film is basically a deconstruction of the entire kaiju and/or sentai genres:
** It reveals that due to Gamera using the Mana Cannon in part 2, more Gyaos are appearing and attacking humanity (in addition, using simple fire balls also cost mana).
** The films before this one portrayed Gamera as a heroic monster who protected humanity from evil monsters. Here, Gamera defeats the Hyper Gyaos, but causes massive amounts of damage and kills many innocent people.
*** The contrast is especially evident when Gamera saves the life of a child. In the Showa Era films, the child saved by Gamera would be happy and cheerful, and their rescue portrayed as a triumphant moment. The boy saved here is crying and terrified, and as he tells his mother that Gamera saved him, the camera pulls back to reveal the destruction Gamera has caused in his battle.
** The film is also much more human driven, since it's about people in a world with giant monsters and Gamera just happens to be the best one.
** The fairly typical "young person who controls/is friends with a giant monster/robot" story is deconstructed in two ways. Anaya has lost her connection to Gamera which has resulted in him becoming far more vicious and callous in his fighting. Irys shows what happens when the young person in that relationship has loads of mental issues; a lot of people end up dead and the young person in question uses their monster for selfish, vengeful reasons.
** The question is raised that Gamera may not actually be protecting humanity, but rather the planet itself. Which of course raises the question of what he'll do when or if he comes to consider humans a threat to the integrity of earth...
* DeconstructorFleet
* DemotedToExtra: Not so much extra, and he is VERY much a major force, but Gamera got a lot less screen time in the third film with only two scenes.
** While he's not shown much onscreen, it mentioned often he's fighting off the Gyaos all over the world for much of the film.
* DestructiveSavior: The destruction that Gamera causes during his battles is shown in explicit, horrifying detail.
* EldritchAbomination: Irys. [[spoiler: There's a disturbing implication that ''Gamera'' is an Eldritch Abomination in and of himself, just one with good intentions]].
* EvilMakeover: While Gamera's not technically evil, his design in this film is much more savage-looking when compared to the previous two films. It helps to symbolize his disconnect from humanity and apparent disregard for the destruction he causes.
* GiantFlyer: Gamera, Gyaos, and Irys.
* GoodIsNotNice: Gamera, while still the good guy, ends up killing hundreds, if not thousands, of innocent people in his attempts to stop the Gyaos.
* GreatOffscreenWar: Gamera's battles against the Gyaos all over the world. The audience only gets to see the fight taking place in Shibuya, with more alluded to throughout the film.
* HotScientist: Nagamine, just like in the first film.
* InfantImmortality: '''Harshly''' averted.
* IWillFightSomeMoreForever: Gamera will continue to fight the Gyaos until his last breath.
* LastOfTheirKind: Gamera is revealed to be this in the opening after the graveyard is discovered.
* MultipleChoicePast: What exactly is Irys? Is it just a mutated Gyaos that happens to be similar to Gamera with its ability to connect to humans? Is it what Asakura claims, and is the safety measure to control Gamera should Gamera become a threat to humanity? Is it another creature like Gamera, created to fight the Gyaos as a last-ditch effort? Is it an attempt to create the UltimateLifeform? Who knows, take your pick.
** Also, what were its motivations? When it shows Ayana all the terrible things it did, like killing her adopted family, was it being malicious or simply showing its mother what it had done for her? Irys certainly has a mean streak, but is it because of or in spite of its connection to Ayana? Irys might have originally been benevolent and just twisted by Ayana's vengeance, or it could have always been a cruel, vicious monster, we just don't know.
** It is pretty clear that at least some of its actions are directly motivated by Ayana's feelings. The clearest example is actually in a throwaway line of dialogue when the authorities are investigating an attack on Ayana's village: it's mentioned that more women were killed than men, by a fair number. Now consider how Ayana and her brother were bullied by girls from school and it becomes pretty clear that Irys was lashing out on Ayana's anger. Whether this is true for all of its actions is unknown though.
* OffscreenMomentOfAwesome: It's mentioned during the course of the film that Gamera is fighting the Gyaos all over the planet. The only one of these battles the audience actually gets to see is the one in Shibuya.
** According to WordOfGod, [[spoiler: Gamera wins the impending final battle against the massive swarm of Gyaos approaching Japan, or at least you're supposed to ''believe'' that he can win]].
* RealityEnsues: The first battle between Gamera and another monster ends in a city being completely devastated, thousands of people dead, and the public calling for Gamera's head on a spike. Indeed, the film takes plenty of time to show the horrific amounts of collateral damage that would be caused by kaiju/sentai battles.
* RiddleForTheAges: Whether Gamera survived the final battle against the Gyaos swarm at the end. [[spoiler: WordOfGod says that it's really a question of whether you ''believe'' he wins.]]
* TheTokyoFireBall: Gamera creates one while fighting the Gyaos in Shibuya. As horrific as it is, the effect actually does look pretty good.
* TurtlePower: It's Gamera.