A killer from ancient times, the Meganulon were a breed of giant insects which escaped extinction by burrowing themselves deep into the Earth's crust. Once there, the beasts stayed locked beneath the surface for millions of years. However, nuclear tests awoke the ancient horrors, who descended on a local mine. The creatures' first victims were a pair of miners, called Yoshi and Goro, who were mercilessly hacked at by the monsters' mammoth pincers. It wasn't long before Yoshi's body was recovered by his fellow workers, while Goro's whereabouts were still a mystery. An investigation was immediately set into place by the authorities, trying to resolve both the murder weapon and the murderer. The authorities returned to the mine shaft where Yoshi was uncovered, dispatching a police officer and two miners, to try and locate Goro. However, the three meet a untimely demise at the claws of another Meganulon that is hiding below the water which has leaked into the area.

The added death toll and still missing whereabouts of Goro prompt suspicion that the missing miner is in fact behind the series of killings. A hunch which is quickly dismissed as one of the Meganulon ventures into a local village to attack a couple, Kio and Shigeru, who flee to get help. Shortly after, the police arrive on the scene and ineffectively try and shot the giant insect down while it bids a hasty retreat back to its lair. The police are quick to pursue, but their weapons pose no threat to the thick carapace of the ravenous insect, whose deadly pincers take the lives of two officers who advance too close. The Meganulon then returns to the mine shaft, killing more innocents along the way.

With the killer finally revealed, and the seriousness of the situation grasped, the self defense force is quickly dispatched to the area to exterminate the threats. Armed with mountable machine guns, a few regiments of soldiers, along with Shigeru, march into the mine to hunt down the creatures. While searching for the Meganulon, Shigeru uncovers Goro's body, which had been dragged deep into the shaft. There is little time for grieving, however, as Meganulon start to emerge to fend off the intruders. The military shells the creature with machine gun fire, but to no avail as the carapace, once again, deflects the bullets. Out of options, Shigeru hitches a ride on a nearby mine cart, driving it down the shaft and directly into one of the Meganulon, killing the beast. With a small victory claimed, Shigeru attempts to retrieve Goro's body, but ends up being trapped as another Meganulon emerges just as a landslide blocks his escape. The large rocks continue to pummel the area, knocking Shigeru out and killing the giant insect.

Eventually, the young miner awakens, as Shigeru opens his eyes only to realize that he is now trapped in the Meganulon's lair. Even with the ravenous insects all around, Shigeru's attention is diverted to another object in the room: a mammoth egg. It's quickly discovered that the Meganulon weren't the only creatures awakened by the atomic tests, as the egg hatches to reveal a gigantic pteranodon called Rodan. The red hued monster flaps its still developing wings, as it spies the killer insects that are situated all around it. The beast wastes no time, and quickly begins to devour the nearby Meganulon, as Shigeru can only stumble backwards at the sickening sight. Once full, the infant monster spreads its wings and takes flight, leaving behind it the remnants of the once horrific insects while Rodan would soon prove a far more deadly adversary to the entire globe.