Humanity finally rids themselves of Godzilla, imprisoning him in an icy tomb in the South Pole. All is peaceful until various monsters emerge to lay waste to Earth's cities. Overwhelmed, humanity is seemingly saved by a race of benevolent aliens known as Xiliens. But not all is what it seems with these bizarre visitors. If humanity wishes to survive, they must reluctantly resurrect their most hated enemy, Godzilla.

Inventor Goro Ibuki creates a humanoid robot named Jet Jaguar. It is soon seized by an undersea race of people called the Seatopians. Using Jet Jaguar as a guide, the Seatopians send Megalon as vengeance for the nuclear tests that have devastated their society.

A great duel of supersonic speed.

A ship runs aground on a mysterious atoll leading to an investigation by insurance representative Kusanagi, who discovers an ancient bead that he gives to his daughter Asagi. Meanwhile, ornithologist Nagamine investigates reports of a new species of large bird named Gyaos. As the Gyaos begin to attack, an ancient guardian with a bond to Asagi emerges.

Reporter Goro Maki stumbles upon scientists conducting weather experiments on Sollgel Island in the South Seas. He discovers the island is inhabited by giant mantis and a woman named Saeko who's been cast away since the death of her father. The pair soon find a helpless infant monster that Godzilla must adopt and learn to raise as one of his own.

A submarine expedition to salvage the remains of Mechagodzilla is thwarted by a massive dinosaur named Titanosaurus. An Interpol investigation leads biologist Ichinose to uncover the work of Dr. Mafune and his mysterious daughter Katsura. Aligned with the Black Hole Aliens, Katsura's life becomes entwined with the resurrected machine.

In postwar Japan, Godzilla brings new devastation to an already scorched landscape. With no military intervention or government help in sight, the survivors must join together in the face of despair and fight back against an unrelenting horror.