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Searching for his brother, Ryota stows away on a boat belonging to a criminal alongside two other teenagers. The group shipwrecks on Letchi island and discover the Infant Island natives have been enslaved by a terrorist organization controlling a crustacean monster. Finding a sleeping Godzilla, they decide to awaken him to defeat the terrorists and liberate the natives.
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.
After a meteorite unleashes a three-headed beast upon Tokyo, Mothra tries to unite with Godzilla and Rodan to battle the extraterrestrial threat.
Sawaki is released from prison after serving eight years for murdering a rival gang leader in order to obtain the land rights to a landfill for the Kotaki clan and he discovers that the world has changed significantly in that time. The police have forced the disbanding of all yakuza groups in and around Tokyo and most of the former yakuza have moved on to legitimate jobs. Sawaki is disgusted that his yakuza brothers have abandoned their codes of honor and are abusing their newfound power in the legitimate business world to exploit the poor. Sawaki feels partly responsible for making them so powerful and enabling their corruption, so he decides to follow his traditional code of honor to save the residents of a small town where his former lover lives.
