Kitamatsu is a small mining community in Kyushu. Shigeru works at the coal mines as a safety engineer. He notes how there is a feeling of uneasiness hanging about the mines. He witnesses a fight erupt between two miners as they start their shift - Yoshi and Goro, the brother of Shigeru's fiancée. The supervisor breaks the fight up and reprimands both men, sending them back to the mineshafts. Part of the tension is the fact that No. 8 mine is going far deeper than any shaft that any of the men have ever worked. Among the problems is the fact that the floor in No. 8 has been creeping, a sign that too much coal has been removed from between two strata of rock. Shigeru is analyzing the problem when a call comes into his office - Mine Number 8 has flooded! Shigeru hurries to the scene of the accident.
Two miners were caught in the flood. Shigeru and two volunteers head into the flooded section. They find the mangled body of Yoshi floating in the water. There is no sign of the other missing man - Goro. It is obvious to everyone that Yoshi's death was no accident. What weapon killed the man is not apparent however. Speculation that Goro is the killer immediately runs rampant. Shigeru tries to console Kyo, reassuring her that Goro is not a murderer.
A police officer is led back into Mine Number 8 by a pair of miners. Hearing splashing in the flooded section, the officer and his escorts tie themselves together and proceed into the flooded shaft. Thinking they are hearing Goro, the men close in on the sound. Suddenly, the lead miner is pulled underwater by some violent force, the cop dragged after the doomed man. The last miner cuts the rope before he too can be dragged under and flees back up the shaft. Grabbing the emergency phone, the man starts to call for help, but something monstrous has pursued him and the man screams as it falls upon him. The only witness to the horror of Mine No. 8 is dead.
At the medical inquiry, the doctor realizes that all four bodies bear similar injuries. Two of the men died not of wounds alone, but also from shock. The weapon is still unknown. The news is greeted grimly by police and news reporters alike.
Blaming Goro for the murders, Yoshi's distraught widow cries for Kyo's blood. Some of the widow's friends drag her away from Kyo's doorstep. Inside her house, Kyo weeps. Shigeru arrives and comforts his betrothed. Suddenly, Kyo's belief that something horrible is in the mine is proven true when a huge insect beast bursts through the back door. The lovers flee, Shigeru returning with a mob of miners and police. The insect beast attacks them, bullets having little effect.
As Police Chief Nishimura calls for reinforcements, the insect monster is pursued to the outer coal dump. After butchering two more police officers, the monster escapes back into the mine. Shigeru wants to follow it into the mine, but Nishimura delays him, telling him to wait for the reinforcements. The reinforcements arrive, a column of JSDF troops. With dozens of men and several heavy machine guns, Nishimura and Shigeru lead the hunt into the mine.
Following the beast's trail of carnage, they soon find it in the flooded section, near Goro's half-buried body. Bullets are of no effect, even the machine guns, and the big bug chases the men back up the shaft. Shigeru releases a train of coal cars, slamming them into the insect, killing it. Shigeru leads the troops back down, intent on recovering Goro's body.
Suddenly, a second insect appears near the caved-in area. The soldiers open fire on it, causing an even more terrible cave-in. Rubble kills the big bug, but Shigeru is trapped behind a wall of stone and earth, buried alive. Attempts to reach Shigeru continue for two days when a sudden earthquake complicates matters. Professor Kashiwagi calls Dr. Tsunikowa at a seismographic research center, learning the quake's epicenter was near Kitamatsu. Dr. Tsunikowa suggests they meet at the old Mount Toya road to inspect the quake's effect on the volcano. They find the road wiped out. They also find Shigeru wandering about in a daze in the devastated area.
An examination reveals that Shigeru is suffering from memory loss - he does not even recognize Kyo or a photo of the monster from the mine. Meanwhile, Professor Kashiwagi identifies the bug monster as a species known as Meganuron, thought extinct for millions of years. He expresses hope that the police can remove its carcass from the mine.
Elsewhere, a JSDF fighter pilot reports a UFO to his control tower. The pilot pursues the supersonic object, marveling at the incredible maneuvers it executes at such speeds. The control tower officers are stunned. Soon they are horrified when the object turns and destroys the pursuing plane. Later, the JSDF meet with reporters, still at a loss to explain the tragic incident. A call comes in for Izeki. It is from his news desk; a British cargo plane has also mysteriously crashed with no survivors.
The entire Pacific is alarmed by the rampaging supersonic fiend. Peking, Manila, Wake Island, Rangoon and Singapore all report violent encounters with the UFO. In Kyushu, a more local problem is present; the volcano Mount Toya is again threatening to erupt. Although Nishimura makes the volcano off limits, two young newlyweds desiring a thrill, decide to visit the volcano. Their photography session is cut short when the UFO attacks them from the sky. Later, only a slipper and the camera are found.
Examining the camera's negatives, Police Chief Nishimura is shocked to discover the image of a giant wing. Izeki suggests taking the negative to Professor Kashiwagi. Professor Kashiwagi instantly makes a connection between the picture and ancient pterosaurs.
In Kitamatsu, Kyo has taken in the amnesiac Shigeru. She shows Shigeru the nest of her pet canary as the eggs begin to hatch. Shigeru stares at the egg in horror… remembering.
He is back in the mine, trapped in a giant cavern teaming with Meganuron. He sees an enormous egg which cracks open. Cackling weirdly, the gigantic reptilian bird inside spreads his wings. Soon, the monster is snatching up the terrible Meganuron with its beak, voraciously consuming them. The sight blasts Shigeru's sanity, the dazed man stumbling away from the cavern.
The shock has restored Shigeru's memory. He makes his report to Professor Kashiwagi. He volunteers to lead authorities to the site, to destroy any other eggs which might be there. The team of miners, scientists and police find neither birds nor bugs, but do recover a giant piece of eggshell before another earthquake forces them to retreat back to the surface.
Professor Kashiwagi's analysis shows the shell to be reptilian and at least 20 million years old. Figuring the size of the complete egg, Professor Kashiwagi states the wingspread of the creature to be 500 feet. At a press conference, Professor Kashiwagi announces that the creature is a Rodan, an extinct species of carnivorous flying reptile, and the supersonic UFO that has been terrorizing the Pacific. He further speculates that Rodan was awakened by H-bomb tests after being hermetically sealed in the cavern eons ago. He says that the cavern and Mount Toya are connected underground, recommending a search of Mount Toya to find Rodan.
Shigeru and Izeki join Nishimura and Professor Kashiwagi in making an air-borne search of the volcano, discovering Rodan lurking in a cave near the crater. The helicopter retreats and the JSDF scrambles a flight of jets to bomb the monster's lair.
From the ground, Shigeru and the others watch the attack. They are shocked when Rodan emerges from a nearby hole, escaping the attack and flying into the sky. Their shock is doubled when a second Rodan emerges from the same hole. Nishimura immediately sends one of his men to inform headquarters of the second Rodan. The unfortunate man is killed when the Rodan flies across the road and the slipstream the monster generates sends his jeep crashing into a boulder.
The second Rodan is pursued by JSDF jets, their missiles less than useless. Rodan destroys some of them when he turns on them in midair, but others join the chase and pursue the monster to Sasebo. Rodan retreats into the water beneath Sasebo Bridge. It is a brief respite; soon the monster emerges, destroying the last of his adversaries and the bridge.
Now, Rodan attacks the city itself. Buildings are ravaged by the supersonic monster's slipstream. When he lands, structures crumple beneath Rodan's awesome weight. Men and cars are blown away by the powerful winds generated by his huge wings. Tanks and rocket launchers are unable to harm Rodan and the monster even destroys the façade of the JSDF headquarters. To make matters worse, the other Rodan arrives, increasing the destruction of Sasebo. The monsters finally tire of the carnage, escaping back into the sky. When Nishimura and Shigeru arrive at the devastated headquarters, they are told that the Rodans escaped. More, they have also destroyed the city of Yawata. They have left two cities burning in their wake.
A meeting is called to decide how to deal with the Rodans. As they have not been seen for a week, Professor Kashiwagi states that they must have returned to Mount Toya to hibernate. The JSDF decides to seal off the second exit with missiles while tank shelling seals the crater, burying the Rodans alive. Dr. Tsunikowa opposes the plan, fearing the volcano will erupt. Police Chief Nishimura allays his fears somewhat, assuring him that they will evacuate everyone first. Despite any risks, Rodan must be stopped.
Kitamatsu is evacuated but Kyo insists on remaining behind with Shigeru at the command headquarters. The lovers join the officials and reporters as the JSDF begins its attack.
First, ballistic missiles ravage and seal the secondary exit the Rodans used to escape before. Then, the tanks begin shelling the crater of Mount Toya. The volcano begins to smoke, just as Dr. Tsunikowa feared. One of the Rodans emerges from the smoke, taking to the air, escaping the trap. As the second starts to make her escape, Mount Toya erupts. The blast engulfs the second Rodan. Severely weakened, the second Rodan drops from the sky, calling to her mate as she sinks into a river of molten lava. Unwilling to leave the stricken monster, the first Rodan refuses to save himself. Still calling to his dying mate, Rodan descends, becoming a part of his mate's funeral pyre, refusing to live without the other.
Watching the fiery death of the monsters, Shigeru wonders if he, as a 20th century man can ever hope to die so nobly. He also wonders what greater horrors might even now be stirring in the darkness.