On June 16th, 1994, an expedition to the radiation-infested Adonoa Island uncovered a massive egg, nearly as tall as a fully grown human. As night fell, the team transported the egg back to their camp, planning to study it before bringing it to Japan. They noticed that the egg, dormant since the Mesozoic era, was covered in unusual vegetation. Before the scientists could examine it further, a giant pteranodon named Rodan swooped down to protect it. Fortunately, Rodan became distracted by the sudden arrival of Godzilla. Their resulting battle allowed the scientists to escape with the egg to Japan in a transport helicopter.
The egg, believed to be that of a pteranodon, was moved to the National Institute of Life Sciences in Kyoto. Once there it was assigned for study to biologist Azusa Gojo. The plants growing on the egg were removed and placed in plastic bags for future analysis. However, G-Force engineer and pteranodon enthusiast Kazuma Aoki barged into Azusa's lab. Although Azusa caught him, he managed to steal one of the samples in hopes of creating an excuse to return. His plan was stopped, though, by psychic Miki Saegusa. She sensed a psychic signal from the vegetation, which was actually a prehistoric lotus japonicus plant.
Studying it further, Miki and her students at the psychic school soon harmonized with the ancient plant. Not only that but they were able, through chorus, to reproduce the same signal. However, when a recording of this signal was played, the egg began to glow. As the melody continued, the shell started to tremble before the glass enclosure shattered. Azusa screamed in fear as the egg cracked open. To her shock, instead of a pteranodon, a baby theropod emerged from the egg. While indeed the nest it came from was that of a pteranodon, its egg had been parasitically placed there by a Godzillasaurus.
The newly hatched dinosaur, exposed to mild radiation on Adonoa Island, approached Azusa. Although the biologist was initially fearful, the young Godzillasaurus imprinted on her. Azusa carefully fed the newborn some roses from a tipped-over vase. The baby devoured the plants without hesitation, reassuring the scientists that he wouldn't try to harm them.
However, their peace was short-lived when Godzilla was detected approaching their location. Realizing that Godzilla was attracted to the child, they quickly moved to a secure bunker beneath the facility. They hoped by doing this it would sever their connection and stop Godzilla from tracking the young Godzillasaurus. As the King of the Monsters arrived, clawing at the building above as he roared, BabyGodzilla's eyes glowed red in fear. Azusa stayed close to him, comforting the frightened creature. Fortunately, their theory proved correct: the nuclear menace could no longer sense the baby. Frustrated, Godzilla let loose a heat ray into the air before turning away, returning to the ocean.
Following this incident, BabyGodzilla was moved to a G-Force facility. Once there he was placed in an enclosure designed to mimic a jungle environment. Azusa became his caretaker, treating the ancient creature like a beloved pet. He was tolerant of humans, showing no aggression toward Kazuma Aoki. In fact, he barely reacted when Aoki's personal flying vehicle crashed into the trees of his pen. However, when Miki and the psychic children arrived and sang the chorus that mimicked the one emitted by the plants on BabyGodzilla's egg, the young saurian became overwhelmed. His eyes flashed red, and electronic interference filled the room. Meanwhile, far away, Rodan stirred from his slumber. The winged monster evolved into a more powerful form. Sensing BabyGodzilla, he took flight, on a mission to rescue his adopted brother.
Meanwhile, further research revealed that BabyGodzilla possessed a secondary brain in his hip, which controlled his lower body's movement. G-Force hypothesized that Godzilla also had this organ and that destroying it could cripple the giant. They devised a plan using Mechagodzilla's shock anchors to target and destroy this secondary brain. The plan also called for using BabyGodzilla to lure the King of the Monsters away from populated areas.
As G-Force began to put the plan into action, they ran into trouble when BabyGodzilla refused to board the transport container. The act was causing stress on the young creature, its eyes glowing red. As a result, Azusa volunteered to accompany him, calming the young creature's fear. Satisfied, the container became airborne as a helicopter started to head to an isolated area.
The plan, however, faltered when Fire Rodan intervened. While over the Pacific Ocean, the flying creature quickly destroyed the helicopter transporting BabyGodzilla. The pteranodon then grabbed the container midair. Firmly in his grasp, Rodan traveled next to Tokyo before landing in the city of Makuhari. Once on the ground, the winged monster attempted to open the container with his beak. This was interrupted, though, by the arrival of Mechagodzilla and Garuda. Aiming to get the container out of harms way, the pair engaged Fire Rodan in battle. Although the winged monster was ultimately defeated, peace was short lived as Godzilla arrived on the scene. The King of the Monsters then quickly engaged with its robotic doppelganger, turning the area into a battlefield again.
Inside the container, Azusa and BabyGodzilla could only listen as the epic battle raged outside. BabyGodzilla sensed that the two titanic beings fighting for him were being overwhelmed. As Mechagodzilla's assault tore apart Godzilla, rescuers arrived and began to open the container's doors with a blow torch. Once the doors were loosened, BabyGodzilla burst out, witnessing Godzilla's unconscious body being ravaged by Super Mechagodzilla's attack. Driven by instinct, BabyGodzilla roared for help. Answering the call, a weakened Rodan flew toward Godzilla. Still looking to end the battle, the robotic monster unleashed a Mega-Buster ray. Roaring in pain, the blast sent the giant pteranodon to lightly crash on top of Godzilla. Looking down at his once rival, the winged monster began to transfer his lifeforce. This final act empowered and revived Godzilla. With newfound strength, the King of the Monsters unleashed a devastating attack. Although the robotic monster tried to counterattack, ultimately Super Mechagodzilla was obliterated in a blast of crimson energy.
Azusa, heartbroken, realized there was no other choice now. If BabyGodzilla remained in human care, the nuclear menace would continue his rampage to secure him. She tearfully said goodbye to her adopted "Baby" as she left in a helicopter, urging him to join his own kind. BabyGodzilla hesitated, retreating in fear from the towering Godzilla. Azusa, pleading with her friend Miki Saegusa, asked her to telepathically reassure the child that Godzilla meant no harm. Miki's calming words convinced BabyGodzilla to approach the massive creature. The two then swam off into the horizon together, the King of the Monsters gaining a new companion.
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