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Shinjo and his partner Kiyoshi Sato were assigned by G-Force to travel to Birth Island and prepare to initiate "Project T," a plan to use telepathy to control Godzilla. After arriving, Shinjo and Sato encountered Akira Yuki, a vengeful G-Force major who had taken up residence on the island to observe and try to kill Godzilla. Yuki had Shinjo and Sato plant tear gas mines on the shore of the islands, as "practice" for fighting Godzilla. Eventually, a G-Force helicopter arrived on the island, carrying Miki Saegusa, Susumu Okubo, and Chinatsu Gondo, who were to assist with Project T. When Godzilla came ashore, Shinjo and Sato attempted to fire a psionic transmitter into Godzilla's neck. While Godzilla was disoriented from the tear gas mines, the two were able to fire the transmitter into Godzilla's neck. For a period of time, Miki was able to telepathically control Godzilla, but he emitted too much energy and the device attached to Miki short-circuited. Shinjo and Sato then tried to help Yuki fire a bullet filled with blood coagulant called "Yuki's Special," but they were stopped by Miki, who angrily told them that killing Godzilla was not the answer. Suddenly, the skies overhead turned dark and a giant crystalline being touched down on the island, revealing itself as SpaceGodzilla. After SpaceGodzilla and Godzilla battled, Shinjo decided to stay on the island with Miki, while Yuki, Okubo, and Dr. Gondo left for Japan. Shinjo forced Sato to stay on the island as well. One night, while Miki was standing on the beach, Shinjo approached her and remarked that she seemed to care about Godzilla a lot. Miki replied that Godzilla had feelings just the same as human beings, and that stupid men like Shinjo were always blindly focused on killing him.
That night, their camp was raided by the Yakuza, who beat Shinjo and Sato into submission and kidnapped Miki. Shinjo and Sato returned to Japan and met up with Yuki to try and rescue Miki. The three of them tracked the Yakuza down to an abandoned warehouse, where Okubo was attempting to weaponize the telepathic transmitter using Miki. Shinjo, Sato, and Yuki snuck into the warehouse through a manhole, and initiated a gunfight with the Yakuza. During the battle, one of the Yakuza turned over the bed Miki was tied to and used it as cover. Miki used her telekinesis to raise the bed, allowing Shinjo to shoot the assailant in the foot. The Yakuza retreated, and Shinjo untied Miki. Yuki and Sato ran into the room and told Shinjo they had to leave now, as SpaceGodzilla was approaching. The four escaped the building just before SpaceGodzilla flew over it, destroying the building and killing Okubo. Shinjo, Sato, and Yuki returned to G-Force headquarters, where they were met by an impatient Commander Takaki Aso, who ordered them to suit up and pilot the M.O.G.U.E.R.A. and engage SpaceGodzilla in Fukuoka. Along the way to Fukuoka, Yuki diverted M.O.G.U.E.R.A.'s course to attack Godzilla, who was also heading to Fukuoka. Shinjo and Sato knocked Yuki out and tied him to a seat in the back of the cockpit, then resumed their course for Fukuoka. Shinjo and Sato commandeered M.O.G.U.E.R.A. against SpaceGodzilla, but the mecha was knocked into submission and the two were knocked out. Yuki regained consciousness and woke Shinjo and Sato up, and they quickly resumed operation of M.O.G.U.E.R.A. When Godzilla arrived, Shinjo decided that SpaceGodzilla was the primary target, and to avoid attacking Godzilla. Shinjo noticed that Godzilla was attacking the crystal spires SpaceGodzilla had set up around the city as well as the Fukuoka Tower, and realized that Godzilla was trying to destroy SpaceGodzilla's power source. M.O.G.U.E.R.A. split into the Star Falcon, piloted by Yuki, and the Land Moguera, piloted by Shinjo and Sato. The Land Moguera burrowed underground and blasted the supports for the Tower, causing it to weaken. Godzilla noticed and slammed against the tower, destroying it. M.O.G.U.E.R.A. recombined and assisted Godzilla against the weakened SpaceGodzilla, but M.O.G.U.E.R.A. was impaled by SpaceGodzilla's tail and flung into a building. Yuki ordered Shinjo and Sato to retreat in the escape pod, while he dealt with the monsters.
After escaping, Shinjo and Sato encountered Miki and Dr. Gondo, who asked where Yuki was. Shinjo said that he would go and find Yuki, and ran towards the battle. Shinjo saw M.O.G.U.E.R.A. crash into a building, and ran to the wreckage. There, he found Yuki hanging by his foot from a hatch in the mecha. Shinjo aimed his pistol at the hatch, hoping to shoot it open, but suddenly heard Miki's voice in his head. Miki told Shinjo to relax and let her see things through his eyes. Shinjo did as Miki asked, and Miki used telekinesis to open the hatch and release Yuki. After SpaceGodzilla was destroyed, Sato, Miki, and Dr. Gondo found Shinjo with Yuki in the ruins of a building. Shinjo and Miki walked along the shore as they watched Godzilla wade out to sea. Miki asked Shinjo to close his eyes, and when he did, he saw Little Godzilla walking around free on Birth Island, spitting atomic bubbles at the ground.