Plot
Following the events of Godzilla: Planet of the Monsters, the Aratrum is unable to contact Haruo and the rest after their encounter with the original Godzilla. Unberto Mori orders the Aratrum's withdrawal if drones fail to find survivors within 48 hours. Haruo Sakaki is revealed to have been rescued by a native girl named Miana, who treated his wound with a strange powder. Haruo reunites with his teammates Yuko, Belu-Be, Adam and Marco, and they were confronted by who they later learned to be Miana's twin sister Maina before being captured by the latter's hunting party. The group are reunited with Martin Lazzari, whose platoon have been healed by the twins' people (known as the "Houtua"), surviving descendants of humans who remained on Earth and safeguard the egg of their fallen deity.
The group are telepathically questioned by the twins and the Houtua leaders over why they burned their lands, letting them go once Haruo explains they were only attacking Godzilla. Accompanied by Miana and Maina as their protective guides and observers - the twins revealing they can also speak verbally - Haruo's group reunites with Metphies and the other survivors during an encounter with the Servum. During the fight, Galu-Gu realizes that the twins' arrowheads are laced with "nanometal", the nanotechnology used to create Mechagodzilla. Galu-Gu explains that the nanometal somehow survived and expanded itself over the past 20 millennia. Haruo is convinced by Galu-Gu to remain on Earth and resume the plan to kill Godzilla, sending a few crew members back to the Aratrum. The group trace the energy signature to the rebuilt facility that held Mechagodzilla, which Galu-Gu christens "Mechagodzilla City". The twins part ways with the group while warning Haruo that the nanometal is poisonous. the Bilusaludo assure the group that the technology is only harmful to Godzilla.
The team soon finds that the surviving half of Mechagodzilla's head is the source of the nanometal. Galu-Gu accesses Mechagodzilla's brain to construct all necessary materials to trap Godzilla within the city and cover him with nanometal to finish him off with EMP harpoons, overloading him with energy and causing him to explode just like Godzilla Filius did with the EMP Probes. While overseeing the construction (her power-suit modified into one of three Vulture exo-armors), Yuko confesses her feelings for Haruo and kisses him. Feeling slightly ill since entering the city like some of the others, Haruo finds Metphies working in a cave to repair an item with some of Galu-Gu's technology. Metphies cryptically hints that the Bilusaludo's motives are to become monsters themselves due to their obsession with logic and technology, confiding to Haruo the name of a greater being more terrifying than Godzilla that destroyed his homeworld of Exifcalus:"Ghidorah".
As Godzilla awakens and begins heading towards Mechagodzilla City, most of the human members are horrified to learn that most of the Bilusaludo had willingly allowed themselves to be assimilated into Mechagodzilla City to further fortify it. Godzilla's quick advance on the city forces Galu-Gu to sacrifice the city's defenses in order to divert power to finish the harpoon while Haruo, Yuko and Belu-be would be using the three Vultures to slow Godzilla down. Though the trio managed to hold Godzilla for the plan to go underway, Godzilla survives the trap and proceeds to overheat the facility. This forces a defiant Galu-Gu to fuse with the nanometal as the humans escape the city. Galu-Gu then has the Vultures' nanometal absorb their pilots to use them as sacrificial spears to kill Godzilla.
Haruo is unaffected while Yuko is being slowly converted against her will. Metphies warns a conflicted Haruo that Mechagodzilla City will consume Earth if not stopped, and that its destruction could save Yuko, with Galu-Gu arguing that transcending their humanity is the only way to kill Godzilla. Haruo ultimately decides to fight Godzilla with his humanity intact, the destruction of Galu-Gu and the command center rendering the nanometal inert as Godzilla frees himself and destroys the city. Haruo tends to Yuko, who is unable to wake from her comatose state due to the nanometal assimilating her, while the surviving humans hide in a cave with Metphies as everything burns around them.
