Godzilla Junior first appeared in Godzilla vs. Mechagodzilla II as an egg. Presuming it to be a Pteranodon egg, a scientific team unearthed it from Adona Island and shipped it to Japan for study. The egg displayed strange psychic properties, even imprinting itself upon the biologist Azusa Gojo, before finally hatching to reveal an infant Godzillasaurus, who is named Baby Godzilla. When Godzilla later appeared, having sought out Baby through an unexplained psychic link, Baby left with Godzilla, later settling on Birth Island.
By the time of Godzilla vs. SpaceGodzilla, Baby, had by now had grown to almost a third of Godzilla's height. Now known as Little Godzilla, he interacted periodically with the human characters for a portion of the film, taking a particular liking to Major Yuki of G-Force and establishing a psychic bond with Miki Saegusa. Little One was injured and imprisoned in a cage of crystals by SpaceGodzilla upon his arrival to Earth and remained caged until the defeat of SpaceGodzilla by the combined might of Godzilla and Moguera.
Little One continued to grow, and in Godzilla vs. Destoroyah was renamed Godzilla Junior. He had reached nearly half Godzilla's height. Junior proved himself to be quite a capable fighter, successfully defeating Destoroyah, though with difficulty. Junior was seemingly killed during his second battle against Destoroyah at Haneda Airport, where Godzilla and Destoroyah soon fought. However, the radioactivity resulting from Godzilla's subsequent nuclear meltdown reanimated Junior, who appeared in the final shot of the film as the new Godzilla.