Mysterious planes fly overhead as Dr. Hidaka, his daughter Katherine and a reporter named Alex visit an Arctic Eskimo village, conducting their interviews with the natives. Back on the expedition ship, the crew also observe the sinister aircraft. At a US airbase, fighters are scrambled to intercept the foreign warplanes. Fired upon by the Soviets, the US fighters launch missiles at the intruders. One of the Soviet planes is destroyed, crashing into the Arctic ice. A mammoth mushroom cloud reaches into the sky as the fighter-bomber's payload of nuclear bombs detonates. In the Eskimo village, Dr. Hidaka and his companions watch the display, wondering if this is the start of WWIII.
The ice cracks, steam venting into the night. From the fissure an enormous shape emerges. It is the monster Gamera. The Air Force base is unable to contact their fighters and in the confusion, the huge turtle beast goes unreported.
Dr. Hidaka interviews the Eskimo chieftain, asking him about the huge turtles that legend says dwelled on the Arctic continent long ago. As the Japanese prepare to return to their ship, the Eskimo gives Dr. Hidaka a stone inscribed with a picture of a turtle, the very beast Dr. Hidaka was asking about. The chieftain says that it is Gamera, the Devil's Envoy.
Back at the ship, the crew watch as Gamera advances. Too late the order to abandon ship is given. Gamera attacks the doomed vessel, smashing it to pieces and roasting the fleeing crew with his fiery breath. At the US Air Force base, the last message from the ship is received, reporting Gamera's attack. Observation planes are sent out to verify the report, but the find nothing.
In New York, Dr. Hidaka is interviewed about the giant turtle. He says that the monster is Gamera, a beast that had been hibernating for a thousand years until awakened by the detonation of an atomic bomb. Gamera destroyed their research ship, only the three of them who were not onboard survived. Hidaka says Gamera should die soon from radiation poisoning, though he regrets the loss of such a unique specimen.
In Japan, an old farmer is shocked by the sight of a ball of fire flying in the night sky, one that changes its direction. All over the world, the same flying saucer is reported.
On the plane back to Tokyo, Alex remarks how Gamera has been replaced by flying saucers in the news. The reporter tells Katherine how it is only because he wanted to be with her that he was not on the ship with the other reporters when Gamera attacked. He feels almost that he owes Katherine his life.
Elsewhere, a school teacher shows the older sister of a boy named Kenny a drawing of a turtle Kenny drew. He says that the boy is obsessed with turtles, drawing them all the time and taking his pet turtle to school with him. At dinner that night, Kenny tries to sneak food away for his turtle, but is caught by his sister Nori. It is the last straw for his father Sakurai, who tells Kenny to set the turtle free, otherwise he will throw the animal away while Kenny is at school. Distraught, Kenny goes down to the beach with his turtle. The boy sees Gamera, who looms over the beach. Kenny runs into a nearby lighthouse. As his family watches, Gamera batters the lighthouse, the boy hanging from the broken tower. Gamera sees the imperiled child and grabs him, setting him down on the ground. Kenny and his family thank the monster for sparing the boy as Gamera lumbers back into the sea. Kenny insists that Gamera must be a good monster.
Dr. Hidaka is summoned to Hokkaido to meet with officials because of Gamera's return.
Meanwhile, Kenny returns to the beach, searching the rocks for the place where his pet turtle Tibby is hidden. The boy finally finds the turtle, scolding it for hiding from him and telling it that he will be back the next day.
Gamera is soon sighted advancing on a geo-thermal power plant. Dr. Hidaka meets with army officers to debate what is to be done to stop Gamera. It is proposed to try and employ the steam vents at the power plant, but Dr. Hidaka doubts it will be of use. Instead, Dr. Hidaka hopes to use electricity. At the power plant, Gamera walks into the powerlines, but he is unharmed. In fact, he seems to draw energy from the shock. The army opens fire on the monster, but Gamera is impervious. He sets about destroying the power plant, causing massive explosions and fires. The scientists watch in horror as Gamera consumes the flames.
Dr. Hidaka meets with Professor Murase, discussing the monster. Murase says that the monster's body must be stronger than metal. He is also not sure that the carvings on the Eskimo stone represent ocean waves or something else.
As Kenny cheers Gamera on, the army prepares to use a battery of UN missiles against the monster. Dr. Hidaka and Professor Murase convince the JSDF commander to call off the attack, since it cannot harm the monster. Hidaka wonders if cold might be used against the turtle. The army has a secret weapon, a bomb that can freeze almost anything, though effective for only 10 minutes. As Gamera leaves the ruins of the power plant, the army places charges in his path. The freezing bombs do their work, turning the monster into a frigid mass, slowing him down. The charges blast the ridge Gamera is on, knocking him down and onto his back.
Gamera is finished, Hidaka says. Turtles are unable to flip themselves over and he is bound to die now. Suddenly, Gamera pulls his head and feet into his shell. Jets of flame erupt from the openings and the shell begins to spin. Gamera lifts into the air, flying away. Here, then, is the flying saucer seen all over the world. The lines on the stone were not waves but clouds.
Kenny is caught with stones by his sister. The boy says that he is going to build a house for Gamera. Kenny and his family go to Tokyo to stay with an uncle while their own home is rebuilt. They visit Dr. Hidaka, Kenny again telling the doctor that Gamera is good and kind. Later, a Tokyo boy throws away another batch of Kenny's stones, the boy stubbornly insisting that there aren't any stones like those the bully threw away when his sister and uncle offer to replace them.
Dr. Hidaka recaps what is known about Gamera, his abilities and his habits. He speculates that Gamera is drawn to energy, feeding on sources of power. If he is not killed, it could mean the end of the world.
Strange phenomenon at sea are laid to Gamera's presence. Leading scientists from all over the world arrive to investigate. It is decided to employ Plan Z against Gamera, a peaceful experiment developed in joint cooperation with the USA and USSR. Dr. Hidaka is unsure if it can be diverted for a military enterprise.
Controllers at Haneda airport are alarmed when radar picks up Gamera heading for Tokyo. The monster wrecks havoc upon the airport, destroying it utterly. Then, the giant turtle sets upon the city itself, crushing buildings and using his fiery breath to burn the fleeing populace. Even Tokyo Tower falls before the wicked monster's rampage. Nori tries to get Kenny to evacuate, while the boy stares at Tokyo, telling Gamera not to do anything bad. In the confusion, the boy slips away.
It is decided that the UN will supervise the Z Plan. It will take 24 hours to get everything ready. Dr. Hidaka postulates that Gamera is so aggressive because he is hungry. They decide to feed Gamera, bringing petrolium to the monster via rail cars, hoping to keep him docile until Z Plan is ready.
The engineers and soldiers begin sending oil tankers along the railway to Gamera. During the operation, an engineer spies Kenny aboard one of the oil tankers that is heading toward Gamera. The engineer risks his life getting Kenny off the train car, thwarting the child's plans to reach Gamera and saving his life. Scolded and laughed at, Kenny is sent home.
Z Plan is at last ready. Dr. Hidaka says that the only way to get Gamera to Oshima is to leave a trail of burning oil on the water. Drawn by the flames, Gamera will reach the site.
At Oshima, the fuel arrives. Kenny has stowed away in a crate bound for the Z Plan site. He is soon discovered and brought to Dr. Hidaka and the custody of Katherine.
The oil slicks are released in Tokyo Bay and set on fire. The flames work as expected and Gamera stalks away from Tokyo and swims toward Oshima, devouring the flames. A sudden change in the course of a typhoon complicates matters, the howling wind and rain threatening to douse the flames. Just before Gamera reaches land, the fires go out and he starts to turn away. Alex tries to set some buildings on fire, hoping to draw Gamera back. Dr. Hidaka orders everyone to help the effort. Once a good blaze is going, Gamera turns back, striding onto the beach. An increase in the rain thwarts even this lure, quenching the fire.
Just as Gamera is about to leave, Mt. Mihara erupts. The intense heat of the volcano brings the monster back, keeping Gamera in the area of Oshima.
Kenny is reunited with his sister. They are at hand as the Z Plan is revealed. Flames set about a large platform draw Gamera into position. Once on the platform, the sides of a vast capsule close about Gamera, trapping him. The capsule is set at the head of an enormous rocket. The rocket is launched, sending the trapped Gamera into outer space.
Everyone is relieved that the Mars rocket has worked. Even Kenny, who vows to become an astronaut so he can visit Gamera one day.