A submarine expedition to salvage the remains of Mechagodzilla is thwarted by a massive dinosaur named Titanosaurus. Biologist Akira Ichinose is brought in by Interpol as an investigation is launched. Ichinose's inquiry leads to him to meet Katsura Mafune and uncover the work of her seemingly late father, Dr. Mafune, a brilliant scientist shunned by the scientific community. Dr. Mafune is revealed to be aligned with the Black Hole Aliens, who seek to unleash a reconstructed Mechagodzilla along with Titanosaurus on Tokyo and defeat Godzilla. As Ichinose attempts to reach Katsura, her life becomes entwined resurrected machine.