In a towering skyscraper, an old Japanese woman watches as a storm thunders above Tokyo. She remembers back, to a day long ago when all the mighty towers fell and a primordial horror stalked the land.

In Tokyo, a strange slab is discovered in a construction site. The old woman's father is in charge of examining the slab for the university, trying to decipher the strange pictoglyphs carved on the stone. While the scientist argues with the construction foreman Helzer, one of his assistants examines a strange hole in the slab, suddenly, the man's arm is seized by a monstrous worm. Professor Yoshiwara hurries to slay the thing with a pickaxe. His terrified daughter watches in shocked silence. Yoshiwara soon becomes obsessed by the slab and strange reports from around the globe - reports of a giant flying creature in the skies of the Orient, plagues of locusts, sea monsters. Yoshiwara has deciphered the runes on the slab. They tell of an 'Age of Monsters' and he is convinced that the stone is drawing those creatures to it. He meets his superiors at the construction site where they plan to move the slab to the university. Yoshiwara tries to convince them to dump it into the sea before the monsters are drawn to it. He tells them that several of the beasts have already awakened; Soran, the thunderbird; Inagos, the locust-king; and the fire monster Godzilla. He is, naturally, not believed.

Yoshiwara returns home, having been fired, and wonders how he can warn the rest of the world if even his closest friends won't believe him. The sudden appearance of locusts outside convinces him that it is already too late. Yoshiwara gathers his wife and daughter and tries to leave the city. Congestion forces him to abandon the taxi he has hailed and the family flees on foot. At the waterfront, there is a horrible sight. The bay is filled with squirming, dying sea creatures, as if all the fish in the sea have been frightened into the bay. Moments later the source of that terror rises from the bay, Godzilla.

Godzilla stares at Tokyo's towering buildings, enraged at the change from the lush world he remembers. The radioactive monster blasts the nearest buildings with his fiery breath. Yoshiwara's family escapes on a stolen motorcyle, and soon arrives at the construction site. Everyone except Helzer has left. Yoshiwara decides that they have to use the two helicopters at the site to take the slab and dump it out at sea. Helzer will take the slab, while Yoshiwara distracts Godzilla with the second helicopter. Yoshiwara says farewell to his family and takes off in the aircraft. Godzilla continues to advance, drawing near enough to menace Yoshiwara's fleeing wife and daughter. The frenzied man screams at the monster, driving his helicopter into Godzilla's head. The explosive collision staggers Godzilla, but the monster quickly regains his feet, noticing Helzer's helicopter and the slab. Godzilla turns to chase after the slab, inadvertently toppling a building and burying Yoshiwara's wife beneath a pile of brick and stone. Godzilla pursues Helzer out into Tokyo Bay. Helzer tries to drop the slab only to discover that the release is jammed. The sudden appearance of Soran jostles the aircraft, freeing the slab. The stone pitches into the deep, both Godzilla and Soran diving after it. The thunderbird is soon forced to give up on the chase, but Godzilla follows it into the darkest depths. Amid the ruins, little Noriko Yoshiwara discovers one of Godzilla's scales.

The storm continues to soak modern Tokyo. Noriko Yoshiwara stares, holding the discarded scale of Godzilla. The scale has unlocked for her the secrets of Godzilla's biology. She wishes the monster a long sleep, because if he awakens, she will be waiting for him.