A pteranodon mutated due to the horrors of the atomic age, Rodan emerged from a coal mine, where it began to feed on prodigious arthropods called the Meganulons. Once the young reptile had fed, it soared into the sky. Slicing the air at supersonic speeds, the aerial monster annihilated a jet fighter and proceeded to soar across the globe, sparking unprecedented reports of UFOs across two continents. The beast eventually returned to Japan, where it gained an appetite and quickly feasts on a newly wed couple followed by a heard of cattle.

Meanwhile, another Rodan is discovered, while the Self Defense Force scramble to meet the threat. Their first assault involves a squadron of F86F Saber jets that attack the airborne fiends in the sky, but fails to defeat either menace. One monster lands in an urban area, where the JSDF unleash its full arsenal of tanks and missile launchers, but to no avail. Suddenly, the second Rodan appears, and the two titans take their leave for their home in Mt. Aso. A desperate plan of action is soon concocted: controlled eruption! The JSDF deploy Honest John Missile Launchers which pound the volcanic mountain and cause an eruption. The molten rock sets one of the monsters ablaze, as its mate joins its fallen ally in its dying moments.

Eventually Rodan, possibly a child or one of the Rodans from 1956 that survived, emerges from the volcano some eight years later. The winged terror first battles Godzilla, who had recently awoken, across Japan in a series of stand still fights. While in the middle of a skirmish, the pair are interrupted by Mothra, who uses her webbing to halt the two from fighting temporarily. The three monsters initiate in a long discussion, as the small larva desperately tries to convince the two to focus on a much more dangerous foe: King Ghidorah. Mothra's plea falls on deaf ears, however, as both Rodan and Godzilla desire to continue their fight. Having failed her mission, the benevolent insect leaves the two monsters to do battle with the space demon alone. However, shortly after engaging with Ghidorah, both Rodan and Godzilla, having a change of heart, arrive on the scene to aid the small Larva. Together, the three combatants claim victory over the space monster, who is sent into a hasty retreat back to space.

Later, Rodan is summoned by the duplicitous Xilien race from the remote Planet X. Along with his now ally Godzilla, they engaged in heated combat with King Ghidorah on alien soil. The dynamic duo prevailed, and shortly thereafter, the Xiliens revealed their true intentions when they forced the monsters to attack Earth along with King Ghidorah, whom they controlled all along. When the control over these monsters was broken through the use of the A-Cycle Light Ray; Rodan once again joined his ally and repelled King Ghidorah, who returned into the cold void of space.

In the year 1999, Rodan is found peacefully living with his fellow Earth monsters on Monsterland. Eventually, another terrible alien race, calling themselves the Kilaakian, took control of the island and all of its inhabitants. Rodan was the first to attack under the control of his new masters, and renders Moscow a ruined city. Some time thereafter, Rodan joined forces with Godzilla, Manda, and Mothra in the annihilation of Tokyo... but luckily, humankind was becoming wise to the secrets of the Kilaakian. Using the Moonlight SY-3, the JSDF destroyed the transmitter on the moon and effectively severed the mind control. Humankind, now controlling the monsters, sent Rodan to fight against King Ghidorah, who is brutally murdered in the subsequent battle. Though it appeared as though the greatest foe was conquered, the Fire Dragon, a conflagrant UFO, arrived and engaged Rodan in battle. Though Rodan failed to repel the craft, the Moonlight SY-3 extinguished this final obstacle, and the monster was returned to his island home to live out the rest of his days in peace.