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.
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.
The Americans are swiftly closing on Okinawa, an island just south of the Japanese mainland. The Imperial command sends top generals and several army divisions to defend it at all costs. The mission quickly degenerates as vital resources and troops are diverted to other islands. After a civilian evacuation ends in tragedy most of non-combatants are forced to remain on the island. Many convert to soldier status. Tokyo sends mixed messages that squander time and resources, as when they order the defenders to build an airstrip for aircraft that never come. The truth soon becomes obvious: the high command decides that the island cannot be held and effectively abandons the Okinawan defenders. When the Americans land many troops are deployed in the wrong places. As the slaughter mounts, a suicidal attitude takes hold. Okinawa becomes a death trap, for civilian volunteers and non-combatants as well.
The film consists of re-edited material from the original television series Ultraman. Episodes 1, 8, 26, and 27 were used for the film. They were narrated by Hikari Urano as an "Ultraman Documentary". Allegedly only one new scene was shot, and that some parts of the movie where shot in black and white for unknown reasons. The movie screened at the same time as the Toho movie King Kong Escapes.
After a meteorite unleashes a three-headed beast upon Tokyo, Mothra tries to unite with Godzilla and Rodan to battle the extraterrestrial threat.