Workers from the World's Fair are interested in an embedded statue and try to remove it. Gamera arrives and attempts to prevent the removal of the statue, only to be shot at by the crew instead. The statue is removed from the island successfully after a volcano erupts.
After the statue is removed, Jiger makes her first appearance and gets Gamera's immediate attention. The first of several fights ensues, and Jiger wins by shooting projectile quills from her face. The quills impale Gamera's arms and legs, piercing all the way through and preventing Gamera from withdrawing his limbs into his shell and taking flight. To make matters worse, Gamera is on his back and cannot move. He pulls himself up with his tail using a large rock and then removes the offending quills from his limbs and is finally able to fly after Jiger.
Meanwhile, Jiger is actively seeking the statue, because it is making a horrible ringing sound that is causing her tremendous pain. Jiger lets nothing impede that hunt as she splits two ships in half and starts tearing through Osaka. Scientists are beside themselves as Jiger displays another weapon: a heat ray that vaporizes not only flesh but entire city blocks. The JSDF does make a token effort to kill the kaiju, but her quills knock down the F-104 fighters, ending that involvement.
Gamera returns for round two as the fight is witnessed by several children. Gamera knocks Jiger around and appears to have the upper hand until Jiger pulls Gamera to her. Jiger extends a stinger from her tail and inserts the barb into Gamera's chest, laying an egg inside his lung. Gamera staggers away, roaring in agony. Finally, he barely makes it to the bay and his body turn a chalky white color, almost like ice. Gamera is presumed to have been killed at this point as Jiger heads straight to the World's Fair. Jiger finally obtains her goal of the statue, and throws it into the ocean, ending the painful noise.
The scientists were checking out possible causes of the noise, as it affected humans, causing temporary insanity. The children convinced them to do a medical exam on the comatose Gamera, where it's discovered that there's a dark spot on one of his lungs. One of the scientists served as a zoo director and realized that the spot might not be a fast spreading cancer, but actually a Baby Jiger growing in Gamera's lung. An operation was needed to remove the threat, so the children took the initiative by taking a walkie talkie and a mini-sub. Communication is established with the kids and they enter Gamera through his open mouth, and after almost going into his stomach, they arrive at the problem lung. The children are able to exit the sub and walk around in the lung. There, they discover the baby.
The baby looks like its mother, except that instead of shooting quills, the baby squirts sticky goo. But, the baby has a weakness just like its mother: white noise. The kids discover this is actually a fatal weakness and manage to kill the baby using static from their radio. They leave Gamera's body and report their findings to the scientists. They rig up large speakers to keep Jiger at bay, as well as figuring out that power would have to also be run into Gamera, who cannot recover on his own. The children make a final trip inside Gamera to hook up a set of power lines directly to his heart.
Jiger is kept still by the speakers playing the white noise. It's not enough to kill Jiger, but buys enough time for the other plan to start. Gamera is subjected to high voltage shock before the electrical grid overloads. It's enough that Gamera revives on his own.
Gamera flies over to the World's Fair for the final battle. Jiger tries every weapon she's got, but Gamera merely retracts into his shell when the quills start flying. Jiger then uses her heat ray. It doesn't affect Gamera's shell or even skin. Gamera body-slams Jiger several times from great heights, but Jiger isn't really affected. However, it buys Gamera the time needed to go into the ocean to retrieve the statue from the sea floor. Jiger, enraged by the statue's return attempts to impregnate Gamera again. Gamera uses the statue to crush Jiger's tail, destroying the stinger. Gamera taunts Jiger with the statue, who tries in vain to catch Gamera and retrieve the statue. Gamera finally ends the fight by throwing the statue at Jiger, which embeds itself in Jiger's skull, killing her.