A team of scientists are trying to perfect a weather-controlling system. Their efforts are hampered by the arrival of a nosy reporter and by the sudden presence of 2-meter tall giant mantises. The first test of the weather control system goes awry when the remote control for a radioactive balloon is jammed by an unexplained signal coming from the center of the island. The balloon detonates prematurely, creating a radioactive storm that causes the giant mantises to grow to enormous sizes. Investigating the mantises, which are named Kamacuras, the scientists find the monstrous insects digging an egg out from under a pile of earth. The egg hatches, revealing a baby Godzilla. The scientists realize that the baby's telepathic cries for help were the cause of the interference that ruined their experiment. Shortly afterwards, Godzilla arrives on the island in response to the infant's cries, demolishing the scientist's base while rushing to defend the baby. Godzilla kills two of the Kamacuras during the battle while one manages to fly away to safety, Godzilla then adopts the baby.
The baby Godzilla, named Minilla, quickly grows to about half the size of the adult Godzilla and Godzilla instructs it on the important monster skills of roaring and using its atomic ray. At first, Minilla has difficulty producing anything more than atomic smoke rings, but Godzilla discovers that stressful conditions (i.e. stomping on its tail) or motivation produces a true radioactive blast. Minilla comes to the aid of Reiko when she is attacked by a Kamacuras, but inadvertently awakens Kumonga, a giant spider that was sleeping in a valley. Kumonga attacks the caves where the scientists are hiding, and Minilla stumbles into the fray.
Kumonga traps Minilla and the final Kamacuras with his webbing, but as Kumonga begins to feed on the deceased Kamacuras, Godzilla arrives to save the day. Godzilla saves Minilla and they work together to defeat Kumonga by using their atomic rays on the giant spider. Hoping to keep the monsters from interfering in their attempt to escape the island, the scientists finally use their perfected weather altering device on the island and the once tropical island becomes buried in snow and ice. As the scientists are saved by an American submarine, Godzilla and Minilla begin to hibernate as they wait for the island to become tropical again.