Continuing after the end of the events of ''Godzilla vs. Mechagodzilla'', Interpol agents, led by Inspector Kusaka, search for the pieces of Mechagodzilla at the bottom of the Okinawan Sea. Using the submarine, ''Akatsuki'', they hope to gather information on the robot's builders, the alien Simeons. The ''Akatsuki'' is suddenly attacked by a giant aquatic dinosaur called Titanosaurus (Godzilla) and the crew vanishes.