On the relatively peaceful Adonoa Island in the Bering Sea, careless radioactive waste dumps took place. Nobody seemed to care as the island's vegetation and animal life slowly died out. However, two ominously large eggs began to absorb the radiation and grow abnormally. These eggs belonged to a small population of ancient reptiles. The first to hatch was a young Pterosaur. The little creature fed on what little food it could find on the barren island, constantly protecting its unhatched "brother." The Pterosaur grew larger and larger from the radioactivity, until finally it had become the enormous creature Rodan. As a first act, the mighty flying monster attacked a group of people who had come to investigate its home island. The humans had disturbed the other egg, and the unborn baby inside had called out to Rodan and, unknowingly, the only other member of its species. Rodan terrorized the camp, finally resting on a mountain to watch the humans flee. However, victory was not his. The cold waters of the Bering Sea flashed and boiled, and suddenly, a mighty beam of devastation struck Rodan's perch, nearly hitting the pterosaur himself. Rodan flew into the air as Godzilla rose from the sea. Rodan bombarded Godzilla with terrible winds, but the monster king strode ashore to claim the egg that had called out to him. Godzilla and Rodan battled horrendously while the humans loaded the egg into a Helicopter and began to escape. Rodan had tried his best, but Godzilla had proven too strong for the flying reptile. Rodan fell, near death, to the ground as Godzilla left, slowly following the promise of one of his own.

In Japan, samples of some plants found surrounding the surviving egg reveal a kind of psychic music. When played, the egg finally hatches, and instead of a baby pterosaur, it is revealed that Rodan's "brother" was, in reality, a Godzillasaur. After Godzilla battles with Mechagodzilla, this music is sung by a small group of psychic children from the ESP Research Institute at the UNGCC. Baby Godzilla is given a sudden power boost, and tries to break loose from his cage. However, he wasn't the only one to benefit from the plant's ancient music.

Meanwhile on Adonoa Island, amongst the fallen boulders and tattered remains of small mountains, a creature called out weakly. Rodan opened his eyes as he felt himself growing stronger. He took flight and cried out once more as he became Fire Rodan, ready to claim back what was his.

Rodan was left incapacitated by Godzilla's heat ray on Adonoa Island. In its unconscious state, the distant sound of a familiar chorus beckoned. The children of the ESP Research Institute recited the song of the ancient plant that crept on the shell of Baby Godzilla's ancient egg, and Rodan's power suddenly increased. Rodan became Fire Rodan.

The newly charged pterosaur flew over the open sea, ever focusing on one goal: to reach its "brother" Baby Godzilla. Over the urban sprawls of Japan it soared, searching. Finally, it located Baby Godzilla, being transported via helicopter as bait for Godzilla. Rodan quickly annihilated the helicopter and caught the plummeting container, in which Baby Godzilla and his protector Azusa Gojo were being transported. Clumsily, Rodan pecked away at the container, attempting to reveal its contents. Mechagodzilla soon arrived, and the winged reptile turned its attention to this new foe. Rodan fired its uranium heat beam at its towering target. Mechagodzilla countered with a Mega Buster, but Garuda suddenly appeared. Rodan quickly sent the bulky jet crashing into a building, and its attention returned to Mechagodzilla. Its heat beam crashed into the mammoth mech, and Mechagodzilla countered with its plasma grenade and mega buster. Rodan rose from the attack and began to peck at Mechagodzilla's right eye, but the poor creature was soon repelled by the powerful plasma grenade. It appeared as though Fire Rodan was down for the count.

Soon after, Mechagodzilla found itself gripped in battle with Godzilla. Mechagodzilla had gained the upper hand when it ruptured Godzilla's secondary brain, and Baby Godzilla quickly became distraught. It called out, and Rodan listened. It regained consciousness and began to flap and gain altitude. It didn't travel very far when it was shot down by Mechagodzilla's mega buster. In a last ditch effort to save Baby Godzilla, Rodan decided to assist its arch rival Godzilla. It landed on the paralyzed reptile and gave up its life energy to revive and enhance Godzilla's state.

Among the dust and glimmering energy, Fire Rodan disappeared in a remarkable display of courage and selflessness. It's "brother" would be saved at any cost.