The story begins in a beautiful seaside town in Shima Peninsula, Japan. Toru Aizawa (Ryo Tomioka), 11 years old, has recently lost his mother in a car accident. He has been melancholy and distant ever since. Then Toru finds a tiny egg on a mysterious red stone. Toru takes the egg in his hand and it cracks. The egg hatches and surprisingly, a cute little turtle pops out. Toru names the turtle "Toto" and decides to raise him. Perhaps Toru's new pet will help to take his mind off the sorrow of his lost mother. Toru's father Kosuke (Kanji Tsuda) runs a local diner and they live in the fairly modest apartment above. Despite this, Toru decides to try to keep Toto a secret. Then strange things begin to happen with the little turtle. Toto grows rapidly, begins to fly in the air, and even blows fireballs! Even with his curious habits, Toto is the perfect pet and friend for Toru. Toru's friend Mai (Kaho) sees Toto and becomes suspicious, because Toto bears a striking resemblance to the giant monster Gamera! Mai recalls that Gamera appeared 33 years ago, and ultimately died defending humans from the horrible attacks of evil monsters. Toru refuses to believe that his little Toto might actually be the giant monster called Gamera! Mai has a more pressing problem. She is going to have a heart operation at a hospital in the nearby city of Nagoya. Concerned, Toru gives Mai the red stone on which Toto's egg was laid as a lucky charm. In the meantime, there has been a series of mysterious shipwrecks... followed by the sudden disappearance of Toto! Toru looks everywhere for Toto, but is unsuccessful. The dreamlike, fun-filled days with Toto, Toru and the kids are gone. But the loss of Toto is momentarily forgotten when Zedus, a gigantic monster lizard, attacks! He begins to wreck Toru's peaceful seaside town, demolishing buildings with every step! Toru tries to escape with his father but his path is halted by Zedus's rampage! Then something stops Zedus's advance... Toru turns to see a 5-meter-tall turtle... It's Toto! However, Toto is still too small to fight against the ferocious Zedus. Toto manages to drive Zedus back into the ocean. Toru is proud, but Toto has used up all his energy _ poor Toto collapses! The government forces sweep in. Councilor Hitotsugi (Tomorowo Taguchi) and Professor Amamiya (Kenjiror Ishimaru) lead a team that captures Toto. Their plan: to use Toto to mastermind attacks against Zedus and save the town. Toru receives a phone call from Mai's parents. Her operation was successful. Toru goes to Mai's hospital in Nagoya to retrieve the mysterious red stone. Whatever the red stone is, Toto knows he needs its special power to help Toto recover. And only Toto can stop Zedus from attacking again!