In the small mining village of Kitamatsu, near the foothills of Mount Aso on the southern Japanese island of Kyushu, two miners have gone missing. The two men, Goro and Yoshi, had brawled earlier that day, and after they entered the mine to start their shift, the shaft had flooded. Shigeru Kawamura, a tunneling and safety engineer at the mine, heads below to investigate and discovers Yoshi's lacerated corpse.
Above ground, a doctor examines Yoshi, and discovers the cause of death to be a series of deep gashes caused by an abnormally sharp object. Some of the miners and their families begin to discuss the possibility of the involvement of Goro in the death.
Two local miners and a policeman are later attacked and slain by an unseen assailant in the flooded shaft. Their bodies are recovered and examined, and the doctor announces that they were also killed by a sharp object. That night, Shigeru and his fiancée Kiyo are attacked by a Meganulon, a giant species of larval insect at Kiyo's home.
The police start hunting the creature, and it kills two officers before escaping into the mine. The police and Shigeru notice that the officers' wounds match the wounds of the murdered. Shigeru, accompanied by police and soldiers, heads into the mine, where they discover the butchered body of Goro and are chased by the insect monster. Shigeru crushes the creature with runaway mine carts, but after another insect monster appears, the tunnel caves in, trapping Shigeru in the mine.
The next day, Dr. Kashiwagi identifies the giant insect as a Meganuron, an ancient species of dragonfly larvae. An earthquake suddenly strikes the area, and rumors begin to circulate that Mount Aso might be on the verge of an eruption. When the police head to the volcano to investigate the damage caused by the earthquake, they discover the only road to the mines has collapsed. But to their surprise they also find an amnesic Shigeru wandering around the epicenter.
Several miles away, in Kyushu, an air base receives an alert from a jet fighter. The pilot reports an unidentified flying object performing impossible maneuvers at supersonic speeds in the vicinity of Mount Aso. Per orders he pursues the object but it swings around and at supersonic speed overflies the jet, destroying it and killing the pilot. After recovering remains of the jet and the pilot's helmet the base gets word that a British airliner has been shot down by an aerial object resembling the supersonic UFO.
Soon after more incidents are reported, from China, Okinawa, and the Philippines of aerial objects causing major destruction and the probability is established that two such objects - still foggily surmised as aircraft, visible only via contrails at ultra high altitude - are engaged in such predations.
Amid constant news reports of these mysterious attacks, a newly married couple disappears around Mount Aso, along with several cattle. When the authorities develop the film from the newlyweds' camera, they discover a photograph of what appears to be a gigantic wing. Immediately ruling out the possibility of aircraft, authorities match the photo with a drawing of a prehistoric Pteranodon and surmise the UFO is indeed a living being, but they want testimony from Shigeru before they can accurately account for these attacks.
Meanwhile, Shigeru's treatment is progressing slowly. One day, in Shigeru's hospital room, Kiyo shows him the eggs that her pet birds have lain. As one of the eggs hatches, Shigeru recalls that he woke up deep within the mine after the cave-in, and found himself surrounded by hordes of Meganuron. In the middle of the cave was a gigantic egg, from which Shigeru watched a massive bird creature emerge. The shock of this memory cures his amnesia.
After descending into the cave with police and scientists, Shigeru finds a fragment of the colossal egg. Dr. Kashiwagi examines the fragment in his lab and calls a meeting with townspeople and members of the Japanese Self-Defence Force. He tells the men that the object seen flying at supersonic speeds is a pterosaur he has dubbed Rodan. Kashiwagi theorizes that nuclear bomb testing may have been the cause of Rodan's awakening.
Rodan emerges from the ground near Mount Aso, takes flight, and heads for Kyushu, with a squadron of the JASDF hot on its tail. After one of its wings is injured, Rodan flies to Fukuoka, where the sonic waves and windstorms from its wings lay waste to the city. Suddenly, the JSDF reports that a second Rodan has been spotted heading towards the city. After leveling the city and leaving the remaining buildings in flames, the two Rodans fly to Mount Aso. The JSDF formulate a plan to have the military fire at the base of Mount Aso, burying the Rodans alive. Shigeru retreats with Kiyo to safety, and the military begins its attack, triggering a volcanic eruption. Mount Aso spews smoke and lava into the sky. The first Rodan's wing is damaged by the eruption; it falls towards a lava flow, where it begins to burn alive. Its mate lives on, but refuses to live without its counterpart, and flies towards its companion, so that both would die together.
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