Time travelers from the 22nd century arrive in present-day Japan with a dire warning: Godzilla will soon return and bring the nation to ruin. These Futurians, including a woman named Emmy Kano, offer a solution. With the help of a writer who has correctly theorized Godzilla's origins, they propose a mission to travel back to 1944 and prevent the creature's birth altogether.

The plan is to relocate a Godzillasaurus from Lagos Island in the Pacific before it can be exposed to the radiation from future American hydrogen bomb tests. The team, which includes the writer Terasawa, uses a time-traveling shuttle to reach the island during a World War II battle. There, they witness the dinosaur being injured by American forces before teleporting it to the Bering Sea, seemingly erasing Godzilla from history.

However, returning to the present, they discover their actions have not saved Japan but unleashed an even greater horror. The Futurians had secretly left behind three small, genetically engineered creatures called Dorats on Lagos Island. Exposed to the 1954 nuclear tests, these Dorats fused together and mutated into the colossal, three-headed dragon known as King Ghidorah. The Futurians' true malevolent intentions are revealed: they aim to use King Ghidorah as a living weapon to destroy Japan and prevent it from becoming a global superpower in the 22nd century.

Realizing they have been deceived, the people of the present scramble for a countermeasure. They believe the relocated Godzillasaurus is still in the Bering Sea and send a nuclear submarine to irradiate and transform it into a new Godzilla to fight King Ghidorah. But the submarine encounters the original Godzilla, who was never truly erased. The Godzillasaurus had already been mutated by a separate, unrecorded Soviet nuclear submarine accident in the Bering Sea years earlier. The newly empowered Godzilla emerges and engages King Ghidorah in a devastating battle.

King Ghidorah initially overpowers Godzilla, but a strike team sabotages the Futurians' mothership, disrupting their control over the monster. This allows Godzilla to turn the tide, decapitating King Ghidorah with his atomic breath and sending his body into the sea. Godzilla then destroys the Futurians' ship before turning his fury on Japan, culminating in a personal confrontation at the headquarters of Shindo Heavy Industries, led by a man who once witnessed and saluted the Godzillasaurus in 1944.

As Godzilla rampages through Tokyo, Emmy Kano returns from the 22nd century with a desperate solution. The Futurians recovered King Ghidorah's preserved corpse and, using advanced technology, rebuilt it into a cyborg: Mecha-King Ghidorah. Now under Emmy's control, this mechanical terror engages Godzilla in a final, cataclysmic battle over Tokyo. Using grappling cables, Mecha-King Ghidorah lifts Godzilla into the sky, but the King of the Monsters fights back, and both titans crash into the sea. While Emmy returns to her own time, Godzilla emerges from the ocean depths once more, roaring his defiance.