Time passes as the once infant Godzilla now begins to grow. No longer known as baby, the monster is dubbed Little Godzilla. The growing child is observed on Birth Island, playing with almost carefree feelings, until the arrival of the sinister SpaceGodzilla. The warped celestial being attacked without remorse against the crying creature, showering its cosmic fires upon the ground. Not until Godzilla showed up, did hope return to Little Godzilla. The aggressive parent fought, but was soon overpowered, leaving the sage scaled baby to feel the wrath of the fanged space monster. Though, SpaceGodzilla did not kill the child, he instead entrapped it in a crystal prison, before disembarking. Mocking Godzilla with the entrapment of his own offspring.

It took the death of the SpaceGodzilla, at the combined might of Godzilla and Moguera to shatter the tomb. Freeing the bewildered Little Godzilla to roam free again.

After the death of the crystal demon, SpaceGodzilla, Godzilla returned to Birth Island, but something was seriously wrong. Either from the overwhelming power of Rodan's life-force or a natural occurring reaction, Godzilla was sent into a nuclear meltdown. His swarming radiation ignited the few uranium deposits on the island, decimating the tropical island. However, Little Godzilla fed off the extreme levels of radiation and grew to a new form, becoming Godzilla Junior.

The animal, though, still possessed its telepathic link with Miki, which was used to lure the germinating monster to Japan. With Godzilla calculated to be in tow, it was hoped that by bringing his offspring to Japan the King of the Monsters would appear to do battle with a new creature, a monster dubbed Destoroyah whose origin lies in the Oxygen Destroyer that killed the original Godzilla more than forty years prior, that was invading Japan. Before Godzilla can arrive, though, Junior is forced to do battle with Destoroyah on his own. Fighting off the ancient evil, Junior suffers a severe blow to his chest before he blasts the creature his ray at close range, sending the monster plummeting into a nearby factory where it was engulfed in flames.

The victory, however, was short-lived. Rising from the ashes of its hellish womb, Destoroyah, in his final form, lashed back. The creature descended into the sky and grabbed Godzilla's son, after toppling the King of the Monsters with his ray. In an act of pure evil, Destoroyah dropped the infant Godzilla, sending the young monster plummeting to the ground, several thousand feet below. The sudden attack managed to, sadly, kill the child monster. Although the creature would not stay dead for long.

After Godzilla reached meltdown, his energy was expelled from his body. As Rodan had done for him two years ago, Godzilla sent what energy he had left to revive his deceased son. The energy coursed through the small monster, breathing life back into it as Junior mutated into a full-grown Godzilla.