The Shobijin, Masami Nagasawa and Chihiro Ohtsuka, visit Shinichi Chûjô Hiroshi Koizumi, his scientist nephew Yoshito Chûjô Noboru Kaneko, and his grandson Shun Chûjô Tatsuki Omori to warn that Godzilla keeps returning to Japan because the government used the first Godzilla’s skeleton in the cyborg Kiryu’s construction. If that skeleton is returned to the ocean, Mothra—the descendant of the original Mothra who attacked Japan forty-three years earlier—will step in to defend the country, taking Kiryu’s place in this ongoing fight.
As Kiryu undergoes repairs and upgrades, its remote pilot Akane Yashiro Yumiko Shaku is sent to the United States for further training, while Kyôsuke Akiba Mitzuki Koga takes her place should Godzilla return while she is away. The government, led by Prime Minister Hayato Igarashi Akira Nakao, is still shaken by the first Mothra’s attack and denies Chûjo’s initial request, yet agrees to discontinue the Kiryu project once the cyborg exterminates Godzilla. When Godzilla resurfaces to assault Tokyo, despite injuries from the last clash with Kiryu, Chûjo and Shun call upon Mothra to confront the rebooted threat and to protect the city.
With repairs completed, Kiryu is deployed but Godzilla defeats both it and Mothra, injuring Chûjo and Shun in the process. On Himago Island, the uncharted volcanic isle in the Ogasawara chain, twin Mothra larvae hatch from their egg and rush to assist their mother. Yoshito Chûjô [Noboru Kaneko], aided by the Shobijin, enters Kiryu via a maintenance hatch to repair it from within the backup cockpit, while the JXSDF forces and the larvae hold Godzilla at bay. In a dramatic moment, Mothra sacrifices herself to shield the young larvae from Godzilla’s atomic breath, and a separate attack damages Kiryu’s maintenance hatch, trapping Yoshito inside. Yet the repairs are completed, enabling Kiryu to wound Godzilla before Godzilla’s roar appears to rekindle its ancient spirit.
The larvae then bind Godzilla in a silk cocoon, and Akiba [Mitzuki Koga] is ordered to kill Godzilla as requested by Yoshito and the Shobijin. Kiryu lifts Godzilla and uses its boosters to carry them both out to sea, while Azusa Kisaragi [Miho Yoshioka], a pilot, blasts open Kiryu’s hatch. Kiryu tilts to allow Yoshito to escape, then sinks into the ocean and drifts toward an underwater trench with Godzilla aboard. Japan rejoices as the monster threat seems contained, and Yoshito bids Kiryu farewell even as the larvae return to Infant Island with the Shobijin.
A post-credits scene reveals an undisclosed laboratory where canisters contain the DNA of numerous monsters, hinting at a broader, lingering danger that lurks beyond the immediate victory.
