Set one year after the devastating clash between Godzilla and Kiryu, the biomechanical Mechagodzilla, Japan is still recovering. Prime Minister Yashiro faces intense pressure regarding the ethics of using the deceased original Godzilla’s skeletal remains as the core
operating system of a weapon. Meanwhile, the Shobijin, tiny twin priestesses of Mothra, appear with a grave warning: humanity’s reliance on Kiryu is an abomination against nature. Mothra agrees to protect Japan from Godzilla in Kiryu's place, but only on one condition—Kiryu must be permanently decommissioned and returned to the ocean grave.Before the government can fully process this ultimatum, Godzilla suddenly reappears, surging ashore to renew his rampage. Despite the moral dilemma, the Japan Self Defense Forces hastily deploy Kiryu into battle alongside Mothra, who arrives from Infant Island to fight the beast. During the brutal confrontation, Mothra is mortally wounded by Godzilla's atomic breath, but manages to lay a large egg before perishing. As Godzilla prepares to deliver the final blow to the fallen moth, her twin larvae hatch early and rush to Tokyo.The infant caterpillars bravely enter the fray, using their sticky silk to bind Godzilla in a tight, restrictive cocoon. However, the combined military and insect forces are not enough to completely subdue the unstoppable titan. Recognizing that humanity must take responsibility for its own sins, Prime Minister Yashiro relents to the Shobijin’s plea and issues a command to spare Mothra's legacy. Yoshito Chujo, the primary engineer maintaining the mecha, boards the disabled Kiryu manually to override the computer lockouts.Kiryu’s pilot, Lieutenant Kisaragi, steers the cyborg into a desperate, final
suicide mission. Kiryu fires its devastating Absolute Zero Cannon point-blank into Godzilla's chest, inflicting catastrophic damage. Rather than executing the monster completely, Kiryu defies its programming, locking its optical sensors into a human-like display of sentience. Carrying out its ultimate redemption, Kiryu seizes the unconscious, heavily bleeding Godzilla in a tight embrace and plunges deep into the crushing depths of the Japan Trench, intentionally burying them both beneath the ocean floor forever. As the threat finally ends, the surviving Mothra larvae safely return to Infant Island, leaving a chastised humanity to ponder the heavy consequences of their scientific arrogance and technological overreach.