With the help of her cousin, Ayana gets a summarized lesson in the guardians of Chinese mythology. Ryuseicho -possibly a Phoenix- is assumed to be the guardian of the South, a Turtle-like creature guards the North, a Tiger guards the West, and a Dragon guards the East. The natural enemy of the South is the turtle guardian of the north. Ayana interprets this as Gamera and finds a common link between herself and the Ryuseicho.

Much further North - in the Shibuya district of Tokyo - a spectacular battle between several Gyaos and Gamera. But for the most part, where Gamera always seemed to protect the people, his primary focus is the destruction of the Gyaos. Aside from the typical destruction of landmark buildings, many people are killed - whether they are crushed underfoot or swept up in the wave of fire that washes over the district. With one small exception (Gamera stops Gyaos's supersonic beam from killing a small boy), it seems as if Gamera has put the well-being of mankind on the backburner and has given the higher priority to destroying Gyaos.

People are shocked, and public opinion of Gamera sinks to a new low. Despite the testimonial of his supporters, Gamera is labeled a menace.

Ayana watches the television news reports of Gamera's destruction and knows she must take action. She visits the cave again, finding a large comma-shaped bead - similar, but at the same time different from the one Asagi Kusanagi had before Gamera was resurrected in Sendai. This also glows at her touch, but behind her something stirs.

Out of an ancient-looking egg hatches a creature that Ayana names "Iris" (after her cat killed along with her parents). She feeds it and looks after it, despite Moribe's warnings. Soon after Iris makes its way outside its cave and Ayana searches frantically in the forest until she find the creature. At this point, a physical transformation occurs as Iris and Ayana form both a physical and psychic bond with each other.

Searching for Ayana, Moribe ventures into Iris' cave. There, he finds that Iris has created some sort of organic chamber and in quite a heroic move, he frees her. In some sort of coma, she is taken to the hospital. Along with the JSDF, Inspector Osako and Nagamine, together again, travel to the Nara district to investigate the decimation of an entire village. Sleeping in the forest, a huge Irys is discovered by some high-school students. The JSDF position themselves around a sleeping Iris. Nagamine finds that some time after being taken to the hospital, Ayana has been kidnapped by creepy game designer Shinya Kurata and government official/temple priestess Mito Asakura - who believe that the entire Iris/Ayana bond has some important religious connotation. When Iris awakens in the forest, the JSDF puts up a meager fight before Iris takes to the sky, looking for Ayana.

Over Kyoto, the JSDF is given the order to attack Iris. Iris begins to fight back, but Gamera interrupts and a mid-air dogfight ensues. The JSDF, still giving Gamera the higher priority, fire a missile at the turtle and knock him off-course. Iris lands in Kyoto with Gamera quick to follow. Gameras blasts are easily deflectd by his new foe and the Kyoto skyline engulfs in flames. Gamera and Iris exchange blows and through Ayana's hate for Gamera, Iris pierces Gameras undershell, mortally wounding our hero. With Gamera fallen and no longer a threat, Iris continues unopposed to bond with Ayana. A strange calm falls over the two as Moribe rushes to save Ayana. Managing to break Iris' concentration and hold on Ayana, Iris simply knocks Moribe out of the way and grabs Ayana for the final transformation!

While trapped in Iris, Ayana begins to understand that her hatred has fueled Iris' killing spree. She questions her own involvement and the real cause of her parents' death by remembering Gyaos. As she slips deeper and deeper into Iris' consciousness, Gamera regains consciousness and rescues Ayana. Not out of danger, an enraged Iris pins Gamera's hand to a giant concrete pillar. Iris begins to drain energy from Gamera and begins to power up her tentacle beams. Trapped and faced with his own destruction, Gamera wells up a fireball burst and severs his own hand! Iris' hold broken, the tentacles let loose a blast of energy. Gamera catches the energy with his stump and collects it until he weilds a fiery new appendage. With this new built up energy, he lunges at Iris and uppercuts through the creature utterly destroying it.

In the aftermath of the battle, amidst the fire and desctruction, Gamera places Ayana down next to Nagamine, Asagi and Moribe. Unable to revie her through CPR, Nagamine looks up to the heavens as the rain begins to fall. Gamera cries out, Ayana regains consciousness and thanks him.

At JSDF headquarters, reports from all over the globe are coming in. Swarms of countless Gyaos are converging on Japan. The order is given: all forces are to assist Gamera. Back in Kyoto, a damaged Gamera marches out onto the fiery battlefield to some very powerful music.