A team of scientists attempts to perfect a weather control system on a distant island. Their efforts are hampered by the presence of 3 giant praying mantises and by the arrival of a nosy reporter. 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 cries for help were the cause of the interference that ruined their experiment. Soon Godzilla himself arrives on the island, incidentally stomping the scientist's base as he rushes to defend the baby. Godzilla kills two Kamacuras during the battle, while one manages to fly away to safety. Godzilla then adopts the baby.
The baby Godzilla, named Minilla (or Minya), quickly grows to about half the size of his father, and Godzilla instructs him on the important monster skills of roaring and using his atomic ray. At first, Minilla has difficulty producing anything more than atomic smoke rings, but Godzilla discovers that stressful conditions, such as stomping on his tail, produces a true radioactive blast. Minilla comes to the aid of Saeko, a female who lives on the island, when she is attacked by a Kamacuras, but inadvertently awakens Kumonga, an ancient giant spider. 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 his son and they both defeat Kumonga by using their atomic rays on the giant spider. The scientists finally use their perfected weather altering device on the island and the once tropical island turns into an Arctic wasteland. Godzilla and Minilla begin to hibernate as they wait for the island to become tropical again. The scientists are then saved by an American submarine.
- Godzilla, the King of the Monsters, who adopts Minilla has a son on Soegell Island.
- Minilla, the Son of Godzilla, who grows to be half the size of his father. He is only able to fire smoke rings, until a large amount of pressure is applied to his tail, and he will fire atomic breath.
- Kumonga, an ancient giant spider who lives on Soegell Island.
- Kamacuras, giant praying mantises who attempt to kill Godzilla, Minilla, and Kumonga. 2 are killed by Godzilla, the other is killed by Kumonga.
- In the English version, Kumonga's name is changed to Spiga.
- In the English version, Kamacuras' name is changed to Gimantis.
- In the English version, Saeko's name is changed to Riko.
- In Japan, the film sold approximately 2,480,000 tickets.