Listening to the tape of the sailors' cries of terror, the government decides to send scientist Ichinose to the home of Dr. Mafune, who studies dinosaurs. Ichinose and an Interpol agent show up at the home, only to be greeted by a very beautiful but stern-faced young woman. Katsura Mafune, the doctor's only daughter, tells the pair that Mafune is dead and that she burned all his notes. Having gotten rid of the two, Katsura goes down to the basement where her amazingly resurrected father is sitting. ;) 

Mafune, embittered by his forced resignation fifteen years earlier, has been driven crazy by the need for revenge. He vows vengeance on the human race. Further into the plot, we find that Katsura, once fully human, was almost electrocuted to death while working with her father on the dinosaur, which they called Titanosaurus. The aliens carried out her lifeless body.They removed her heart, lungs, liver, bowels and all of her other vital organs and replaced them with whirring mechanized parts, making her into a cybernetic organism. She also is able to control Titanosaurus. 

Once underwater, the submarine (with Ichinose still aboard) runs into Titanosaurus. Out of desperation they hit it with everything they can muster...to discover that it can be hurt with supersonic waves. The supersonic frequency sends it reeling, to the dismay to Katsura, who is controlling it! She approaches Ichinose with the notes she claimed to have burned in order to find out just what had knocked the dino for a loop. She relays the answer to her father who grows angry with her for associating with humans. He then sends Titanosaurus to destroy Tokyo.

The aliens note that Godzilla is headed for Japan to fight with Titanosaurus. During the course of the battle, while fleeing from the Defense Force soldiers, Katsura is shot. The aliens salvage her and remove the bullet; then implant the MechaGodzilla control inside her circuit. Mafune, devastated, asks Katsura's forgiveness. Katsura then controls both MechaG and Titanosaurus. 

Ichinose is caught snooping around the Mafune house. He is knocked senseless by the aliens. Coming to, he finds that he is tied up and that his beloved Katsura is responsible for controlling the monsters! Pleading with her father and then Katsura herself, Ichinose is rebuffed. Katsura calls up both monsters to destroy the city. However, the humans are not caught off guard. They manage to shoot an supersonic wave amplifier into Titanosaur's neck andfor the rest of the movie torment him with supersonic waves.

Just as MechaGodzilla is about to blow the responsible helicopter out of the sky, Godzilla saves the day! Godzilla engages in a bloody battle between him and the mountainous metal lizard. Ichinose breaks out of his bonds and he and the Interpol agent manage to kill most of the aliens. Katsura turns a gun on the hapless Ichinose and states, "I'm not alive. I may look like a girl but I'm not...I'm a cyborg!" The Interpol agent shoots her. Ichinose leaps to her side and declares his undying love for her.
Katsura begins to weep uncontrollably...then, remembering, realizes that unless she dies, MechaGodzilla will continue to fight on. She pleads with Ichinose to kill her, but he tearfully refuses. 
She takes the gun she would have used on Ichinose and shoots herself in the stomach, dying in Ichinose's arms.
At that moment, the now headless MechaGodzilla short circuits. Godzilla wipes out MechaG with one blast of radioactive breath. He then finishes off a weakened Titanosaurus. Ichinose watches as a
victorious Godzilla leaps back into the ocean, only taking his eyes off Godzilla to gaze on
the deceased Katsura.

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