A young woman overlooks the ocean as the submarine "Akatsuki" searches for the scattered pieces of Mechagodzilla. Nothing is found as the submarine descends deeper. Suddenly, a massive dinosaur named Titanosaurus emerges from the depths and destroys the sub.At INTERPOL headquarters, the "Akatsuki"'s destruction is discussed along with flying saucers spotted nearby. Akira Ichinose, a biologist from the Ocean Development Laboratory, arrives. He is greeted by his old college friend Murakoshi and made to listen to the "Akatsuki"'s mayday call. Meanwhile, the commander of the Black Hole Aliens, Mugal, meets with his second-in-command, Tsuda, as they overlook Tokyo and prepare their plans to conquer and colonize Earth. Their ally is a brilliant scientist named Shinzo Mafune, whose daughter's life was saved by them. At the Ocean Development Lab, Ichinose learns about Mafune, once a promising biologist who was shunned from the scientific community for his attempts to control life and claiming that he had found a living dinosaur. Ichinose and Murakoshi set out to find Mafune, only to find his property seemingly deserted. They are greeted by the young woman, who reveals herself to be Dr. Mafune's daughter, Katsura. Ichinose and Murakoshi attempt to question her but she evades their inquiry by claiming that her father died years ago. She sends the pair away but Ichinose and Murakoshi suspect she is hiding something.Inside the Mafune house is an underground laboratory where Dr. Mafune is revealed to be discussing with Tsuda about the completion of Titanosaurus' control device. Katsura arrives to tell her father about the men who came searching for him. Mafune scoffs; for him it is too late, as he desires vengeance on the world that shunned him. Tsuda then takes Mafune and Katsura to a hidden base in Mt. Amagi and reveals Mechagodzilla has been salvaged and is being repaired. Mafune realizes his backers are the Black Hole Planet 3 Aliens. Commander Mugal greets Mafune and asks him to provide his controlling device for their new robot, Mechagodzilla 2. Suddenly, a prisoner escapes and makes his way through the forest. He nearly makes it before he is cornered by various alien goons and shot to death.Meanwhile, Ichonese is assisting on the preparations to improve the Akatsuki II. Some of Mafune's notes are found in the archives and reveal that Titanosaurus was originally gentle in nature. Later, Ichinose meets with Katsura and reveals to her that he found some of her father's notes. Katsura tries to convince Ichinose to forget about the dinosaur but he ignores her plea and states that he will be on board the "Akatsuki II". Katsura goes home and is berated by her father for talking to outsiders, reminding her of what her mother suffered. Katsura then tells her father about the research sub's expedition.In an INTERPOL conference room, Murakoshi is given a piece of space titanium. It was obtained by one of their agents, the escapee who managed to give the metal to a repairman before his death. Back at the aliens' base, Mafune is working on repairs to improve Mechagodzilla 2's interface. He mentions to Mugal that if the robot is to be perfect, it needs living brain tissue to control it. Meanwhile, Katsura tries to call Ichinose to warn him not to board the sub. Tsuda arrives and reminds Katsura of the debt she and her father both owe to them. Having suffered a severe lab accident, she was brought back to life as a cyborg. As Tsuda attempts to rid Katsura of human emotion, he has her unleash Titanosaurus against the sub. But before the monster can destroy it, the sub's sonar begins to fail and the sound waves cause the dinosaur to writhe in agony. The "Akatsuki II" manages to escape and INTERPOL deduces that Titanosaurus' weakness is supersonic waves.Ichinose heads off to investigate the Mafune household before having a run in with the disguised aliens. He is saved by Murakoshi as Mugal punishes his men for their failure. Katsura tells her father about Titanosaurus' encounter with the sub and heads out to meet with Ichinose. She desires to gain Ichinose's trust by giving him some of her father's old notebooks. Over tea, Ichinose tells Katsura about the sonic wave oscillator being made to exploit Titanosaurus' weakness to supersonic waves. As the two chat, they are spotted by Miss Yamamoto of the Ocean Development Laboratory. Katsura then reports back to her father with the information, but he is unfazed and sets out to prove Titanosaurus' strength. Against Mugal's orders, Mafune unleashes the dinosaur while the sonic wave oscillator is sabotaged. Katsura stands by as Titanosaurus emerges from the sea and attacks the JSDF. Learning what Mafune did, Tsuda fears their plans will be ruined but Mugal tells him not to worry. Godzilla is approaching and, with any luck, both monsters will be incapacitated, leaving Mechagodzilla 2 to rise unopposed. As Titanosaurus rampages, he is blasted by Godzilla's atomic breath. Katsura is spotted by INTERPOL and shot, causing her to fall off a cliff into the ocean. Mafune then commands Titanosaurus to quickly retreat as Godzilla is left confused.INTERPOL considers Katsura to be dead as Murakoshi and Yamamoto suspect that she had a hand in sabotaging the oscillator. However, Ichinose believes in her innocence and storms off. Katsura's body is recovered by the aliens as their surgeons repair her cybernetics. Mafune is grateful to the aliens for once again saving his daughter's life. In return, he pledges his loyalty to Mugal. Back at INTERPOL, repairs are made to the oscillator as Murakoshi makes plans to head off to Mt. Amagi and investigate the aliens.Back at the base, Mugal reveals to Mafune that, while Katsura has been kept alive, they have installed the control device for Mechagodzilla 2 within her body. Aware that INTERPOL is searching for their base, Mugal has decided to make Katsura Mechagodzilla 2's controller, having heeded the advice that Mafune gave him. Mafune is horrified by what he has done to his daughter and stands beside her as she lays motionless on an operating table. With his daughter unemotive, Mafune breaks down and asks for forgiveness as he realizes how much of her humanity has been lost.Meanwhile, Ichinose returns to investigate the Mafune household but is knocked out by some of the alien guards and brought into Mafune's lab. Tied up, Ichinose comes face-to-face with Mafune as he begs him not to help the aliens. But Mafune says it is too late for him. At Mugal's command, Katsura activates Mechagodzilla 2 just as Murakoshi arrives at the abandoned base in Mt. Amagi. He rescues several prisoners before the base explodes while Mechagodzilla 2 flies off.The aliens command Katsura to control both Mechagodzilla 2 and Titanosaurus as the monsters unleash their fury upon Tokyo. Mechagodzilla 2's new weapons quickly annihilate entire districts of the city as INTERPOL races to complete the sonic wave oscillator. As the two monsters make their way through the city, Godzilla arrives and tackles Titanosaurus. But Titanosaurus pushes Godzilla away with Mechagodzilla 2 opening fire. Together, Mechagodzilla 2 and Titanosaurus overpower Godzilla and drive him into the outskirts of the city. The final repairs are made on the oscillator as Titanosaurus battles Godzilla while Mechagodzilla 2 watches from the sidelines. Godzilla manages to get the upper hand on Titanosaurus but is blasted by Mechagodzilla 2. Titanosaurus continues to soften up Godzilla as Mechagodzilla 2 fires its missiles and incapacitates Godzilla, who is buried underground.INTERPOL completes the repairs on the sonic wave oscillator and loads it onto a helicopter. Murakoshi and his men make their way to the Mafune residence as Ichinose tries to free himself and reach Katsura. The INTERPOL chopper flies over Titanosaurus and bombards the monster with supersonic waves, which damages Mafune's controls. Mechagodzilla 2 prepares to shoot down the helicopter, but Godzilla bursts from the ground and blasts the machine with his atomic breath. The monster charges as the machine unloads a flurry of attacks. But Godzilla powers through and pummels Mechagodzilla 2 while Titanosaurus is incapacitated. Mugal heads off to deal with arriving INTERPOL agents as Ichinose frees himself and strangles Tsuda to death. Katsura arms herself with a gun and threatens to shoot Ichinose as he attempts to appeal to her humanity. She responds in a cold, dissociated manner and nearly kills Ichinose before being shot in the arm by Murakoshi. With Katsura injured, Mechagodzilla 2 short circuits and gives Godzilla the opportunity to take off the robot's head. But the monster is surprised to find a cybernetic brain that fires a laser beam back at him.Mugal returns and opens fire on Murakoshi. Murakoshi retaliates as Mugal uses Mafune as a human shield before escaping. Mortally wounded, Mafune cries out to his daughter with his dying breath. Embraced by Ichinose, Katsura's humanity is restored as she attempts to conceal her cybernetic nature. But Ichinose consoles her and she breaks into tears as Ichinose comforts her that she is still human. Katsura realizes that, since she is Mechagodzilla 2's controller, she must die to destroy the machine. Ichinose cannot bring himself to kill her, causing Katsura to grab her gun and kill herself.Mechagodzilla 2 is disabled and finally destroyed by Godzilla, who then turns his attention to Titanosaurus. Mugal attempts to flee from INTERPOL by boarding one of a group of flying saucers. As the saucers fly away, they are spotted by Godzilla and destroyed with a blast of atomic breath. He then finishes off Titanosaurus as the dinosaur plunges off a cliff into the ocean. Everyone celebrates as Godzilla emerges triumphant. But the victory is a somber one as Ichinose carries Katsura's body on a hill overlooking the sea. He is joined by Murakoshi and the other members of INTERPOL as they pay their respects to Katsura. Godzilla lets out one final roar and heads out alone into the ocean.