Godzilla: Tokyo S.O.S. (2003)

In 2004, one year after the epic battle between Godzilla and Kiryu, Mothra's Shobijin appear to Shinichi Chujo, a scientist who helped to rescue them from Clark Nelson back in 1961. They inform him that it was wrong for the Japanese government to create a weapon using the first Godzilla's remains, and that they must be returned to the ocean or else Mothra will be forced to declare war against humanity. They assure Chujo that if the first Godzilla's remains are returned to the ocean, then Mothra will defend Japan from the current Godzilla in place of Kiryu. The Shobijin then depart with Mothra. Meanwhile, repairs on Kiryu are nearing completion, and the mech will soon be ready to face Godzilla once again should the monster return. The original members of the Kiryu squad are being sent to the United States for further training, and a ceremony for them is being held by the AMF. During the ceremony, Yoshito Chujo, Shinichi Chujo's nephew, notices Kiryu's former pilot Akane Yashiro walk out of the room and into Kiryu's hangar. Yoshito follows Akane and starts a conversation with her. Akane remarks that she feels sorry for Kiryu, as she senses that it does not want to fight Godzilla. Akane tells Yoshito to take good care of Kiryu, then leaves.

Sometime later, the carcass of a gigantic sea turtle washes ashore in Japan. The creature is identified as a Megalo matamata, or "Kamoebas," a giant species of sea turtle discovered on Sergio Island in 1970, and the first specimen spotted since the 1980's. The creature has large claw marks in its neck, leading the AMF to conclude it was killed by Godzilla. As the AMF rushes to complete Kiryu in preparation for Godzilla's arrival, Chujo meets with the Prime Minister, Hayato Igarashi, telling him to scrap the Kiryu project as per the Shobijin's warning. Igarashi acknowledges Chujo's concerns, but states that too much has been invested into the Kiryu project to allow it to be scrapped now. He swears that as soon as Kiryu successfully kills Godzilla, he will have the project ended, but until then Kiryu is Japan's only defense against Godzilla.

Godzilla soon surfaces in Tokyo Bay, easily making his way through the JSDF's defenses and approaching the hangar containing Kiryu. As Tokyo is evacuated and Kiryu is prepared for launch, Chujo's grandson Shun creates a giant version of Mothra's symbol using desks from a school, inspired by Chujo and his friends painting the symbol on an airport runway back in 1961 to attract Mothra. Sure enough, Mothra arrives in Tokyo and attacks Godzilla. Mothra is able to hold her own against the behemoth for a time, but Godzilla eventually overpowers her. Left with no choice, Igarashi orders Kiryu to be launched into battle against Godzilla. Godzilla and Kiryu do battle once again, only for Godzilla to knock the mech out of commission with his atomic breath. On Himago Island, two twin Mothra larvae hatch from an egg and swim to Tokyo to aid their mother against Godzilla. When Godzilla spots the larvae, he fires his atomic breath at them, only for their mother to fly in front of the blast and sacrifice her life to save them. Heartbroken, the larvae battle Godzilla while Yoshito enters the damaged Kiryu and attempts to repair him manually. Yoshito gets Kiryu back up and running, but finds himself trapped inside of the mech. Rather than compromise the mission, Yoshito lies and says he is safe and allows Kiryu to re-enter the fray. Kiryu engages Godzilla again near the National Diet Building, and manages to pierce the chest wound Godzilla sustained a year before with his drill hand. Kiryu rotates the drill and severely wounds Godzilla, then fires his hyper Maser beams into the open wound, causing Godzilla to roar out in agony. Mothra's larvae then cover Godzilla in silken webbing, leaving him immobile on the ground. The AMF orders Kiryu to finish Godzilla once and for all, but the first Godzilla's spirit is reawakened again and takes control. Rather than kill another member of his kind, Kiryu chooses to carry the beaten Godzilla out to sea and sink with him into the Japan Trench. As Kiryu and Godzilla fly over the ocean, several AC-3 White Heron jets fly next to Kiryu to try and rescue Yoshito, whom the AMF has just learned is trapped inside. Kiryu opens a trap door on his body and allows Yoshito to escape and be rescued by one of the planes, displaying a message reading "Sayonara Yoshito" on a computer screen. Yoshito sadly replies "Sayonara Kiryu" and watches as Kiryu plunges into the ocean with Godzilla. Both monsters sink into the trench until all contact is lost. Igarashi declares this a "hollow victory," while the Shobijin are content that the spirit of the original Godzilla can once again rest in peace as they return to Infant Island with the larvae.

In an AMF laboratory, several cryogenic tanks are holding the DNA of various other kaiju including the 1954 Godzilla and a 1987 Kamoebas.