Warning: Contains Spoilers!
In the present, a young boy named Toru has been having a hard time adjusting to the fact that his mother died in a car crash nearly a year ago. Life has been very rough for the boy since then, and he has mostly wanted to stay away from other people for most of the day. The only people who can really cheer him up are his neighbor Mai, or his two friends, Ishimaru and Katsuya. He prefers to stay away from his dad, Kousuke.
One day, Toru is playing alone at a nearby beach, and spots a strange red glow coming from an island not too far away. This island was also near where Gamera had self destructed. Toru heads toward the red glow, to find a tiny egg, and the source of the red glow: a strange red orb with weird markings on it. Toru picks up the egg and is examining it when the egg actually hatches to reveal a baby tortoise! Toru then names the tortoise Toto, and takes him home as a pet, along with the red orb.
Toru has to keep Toto hidden from his father, thirty-eight year old Kousuke, because he is not allowed to have pets. As days pass, it becomes harder and harder to hide Toto from Kousuke, because the turtle is growing drastically larger every day. Toru�s bond with Toto becomes very large, and soon Toru sees Toto as a brother-like figure. Toru begins to think that there is something strange about Toto, and the young boy is correct. The turtle begins to spit tiny fireballs and fly! Toto even scares Mai by flying outside her bedroom window. Mai promises not to tell anyone about Toto, and helps Toru take care of it.
Mai believes that Toto is actually the son of Gamera because of his powers, but Toru refuses to believe that because then he will lose his friend. Toru believes Toto is the only thing he loves that he has left- his mother died, and he has been in emotional isolation from his father for months. Despite Toru refusing the idea, Mai continued to try to convince Toru that he was going to lose Toto, but to no avail.
Toto keeps growing and growing until he becomes three feet in length. Toru realizes that Toto can�t be hidden away from his father in his bedroom anymore- so he and his friends move the turtle to an abandoned beach shack that his friends and he use as a hideout. Unfortunately, Toto flies away and never comes back.
Soon after Toto�s disappearance, a series of bizarre events begin to occur in the Pacific Ocean. One by one, boats sink, and the crew on them are devoured. But by what is unknown. Each boat sank closer to Japan than the one before. Eventually, whatever is causing these strange incidents comes ashore at Iseshima. The thing that caused the ship wrecks reveals itself to be the terrifying kaiju, Zedus. The behemoth goes on a rampage, crushing buildings and devouring humans with amazing speed. Eventually, Toru, Ishimaru, and Katsuya are caught in the center of the chaos and destruction. Zedus corners them and is just about to devour them, when another giant monster enters the fray. The creature is a giant turtle; quite similar to Gamera, and on two legs. But, it is obviously not Gamera- the creature was clearly still a young juvenile. Toru noticed strange markings on its abdomen, the same markings which were on Toto�s.
This creature that now towers over buildings was once Toru�s pet.
Zedus immediately overwhelms Toto with his intense brute force and speed. Toto is eventually forced onto a bridge, and Zedus climbs on top of the bridge�s rails and fires is spear-like tongue, which goes right through the middle of Toto�s hand. Toto is then lifted up by Zedus� tongue, and just when it looks like Toto is about to be swallowed whole, Toto blasts his fire ball straight into Zedus� mouth at the last second- Zedus� tongue released Toto, and Zedus fell off the rails and back into the sea. The kaiju retreated, and left Toto behind. Toto then collapsed on the bridge, and fell unconscious. To Toru�s despair, the military came and took Toto away to a science institute, where he could be studied.
Meanwhile, Mai had to go to a hospital for an operation. Toru had given her the red orb for good luck. Mai�s operation was a success, and she and other patients had been moved deeper into the city so they would not be attacked by Zedus. Ever since the first battle between Toto and Zedus, the orb had started to glow�
Eventually, Zedus returned to Japan. He rampaged through the city, destroying everything in its path and devouring any other thing that lived. Zedus eventually smashes through the science institute where Toto was being held, and the battle begins again. Zedus once again overwhelms Toto, forcing the monster deeper into the city. Toru splits up from his friends in order to find Mai. They believe that the red orb she has could help Toto grow in strength.
Meanwhile, Mai rested in her mattress in the hospital, watching Toto and Zedus battle. Toto was getting bashed around, and it seemed utterly helpless in stopping Zedus. Mai wanted to get out of her mattress, but she was too weak from her operation, and needed to rest. She repeatedly says weakly to herself while holding the red orb in her hand �For Toto�for Toto�� and no one every seemed to hear her. Not until a young girl walked up to Mai. She took the red orb, and stared at Toto in battle with Zedus. �For Toto?� She asked. Mai nodded. The girl began to run, heading towards Toto. Eventually, she was blocked, and had to pass it to another child, who ran the orb towards Toto. The same thing happened with him, and the next one, and next. Eventually, the children passed it down to Ishimaru and Katsuya. They then tracked down Toru, who was having an emotional talk between himself and his dad. Toru was given the orb, and after a long talk, gained his father�s trust. Meanwhile, Toto was sent hurling into a building headfirst- and he got stuck in there. Zedus now could kill him whenever he wished too.
Quickly, Toru raced inside the building, and climbed to one of the higher levels, where Toto was stuck. Toru had been told by his father that Toto would most likely gain the ability to self destruct, like the previous Gamera, once devouring the orb, and would probably have to in order to kill Zedus. Toru had to take that risk though. After one last personal talk with Toto, Toru tossed the stone into Toto�s mouth. Toto had a major increase in power, freed himself from the building, and inflicts blow after blow on Zedus, eventually ripping out his tongue. Gamera then spits out an incredibly powerful fireball, eradicating every bit of Zedus. Toru and everyone else in the city watched in disbelief. Toto roared into the sky, and flew off. Toru said his final words to Toto: �Goodbye, Gamera.�