Kiryu is undergoing repair modifications after its battle with Godzilla. Prime Minister Hayato Igarashi accepts Lead Scientist Yoshito Chujo’s choice to replace the Absolute Zero Cannon with a powerful Tri-Maser.
The Shobijin (Mothra’s twin fairies) warn the Japanese government that Godzilla continues returning to Japan because they used the original Godzilla’s bones in Kiryu’s design. If they return the bones to the bottom of the sea, Mothra would gladly take Kiryu’s place in defending Japan, but if they do not, Mothra will declare war on humanity. Soon enough, Kamoebas, a giant mata mata turtle, is found washed ashore on a Japanese beach. It is determined by the wounds on Kamoebas’ neck that Godzilla killed it. Godzilla and Mothra fight, but Godzilla seems to have the upper hand. With the repairs finished just in time, Kiryu manages to even the odds, but Godzilla still manages to knock out both of its opponents.
Meanwhile, on Infant Island, two twin Mothra larvae hatch from Mothra’s egg, and rush to help their mother. As Kiryu undergoes repairs again, the larvae try to hold Godzilla off, but Mothra is killed by Godzilla’s atomic breath while trying to save the larvae. Just in time, Yoshito and the humans repair Kiryu, who stabs Godzilla’s chest with a drill, causing Godzilla to bleed and roar in pain. The larvae begin to bind Godzilla up in web. Just as Kiryu’s pilot, Azusa Kisaragi, receives the order by Igarashi to destroy Godzilla before the Kiryu project is scrapped, Kiryu’s soul is re-awakened through Godzilla’s roar. The cyborg lifts Godzilla and secures themselves with cables. Kiryu then uses its boosters to carry itself and Godzilla to the bottom of the ocean.
In the film’s post-credits scene, in an undisclosed location, a laboratory is shown, filled with canisters that contain the DNA of numerous Toho kaiju. It is stated in the Japanese version via on off-screen voice giving announcements that a “bio-formation” experiment involving an “extinct subject” is about to take place, implying that the JXSDF plans to create another mecha or kaiju-based superweapon, which could mean that Godzilla or another monster could appear once again. In the Japanese version, Godzilla and Kiryu are seen one more time, roaring as they descend into the ocean.