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Keisuke Shimizu was an archaeologist working in Okinawa, where he and his brother Masahiko Shimizu witnessed an ancient Azumi family, which was interrupted when the Azumi princess Nami had a horrific vision of a monster destroying the world. Afterwards, Keisuke dropped Masahiko off at Gyokusen Cave and then responded to a call asking for his assistance. Keizuke was called to investigate a recently uncovered cave, containing various murals and a statue. Keisuke was joined by fellow archaeologist Saeko Kaneshiro, who determined that the mural contained some kind of prophecy and that the statue was of King Caesar, the legendary guardian monster of Okinawa. Later, Keisuke boarded a plane to Tokyo, and encountered Saeko again, who had decoded the prophecy. According to the prophecy, when a black mountain appeared in the clouds a giant monster would come forth to destroy the world. Keisuke and Saeko met a strange man wearing a trenchcoat and sunglasses claiming to be a freelance reporter, who hoped that they would share more of the story with him so he could report on it. Suddenly, Keisuke and the other passengers witnessed a huge black cloud outside the plane's windows that resembled a mountain, with Saeko remarking that it seemed the prophecy was coming true. When the plane landed in Tokyo, Keisuke offered to accompany Saeko to visit Professor Wagura, who she was hoping could help decode the rest of the mural. Once they arrived at Wagura's laboratory, Keisuke revealed that Professor Wagura was actually his uncle. That night, a mysterious man named Yanagawa broke into Wagura's house and tried to steal the statue of King Caesar. Keisuke fought Yanagawa and eventually forced the thief to run away. The next morning, Mount Fuji unexpectedly erupted and "Godzilla" emerged from the volcano, beginning a rampage across the countryside. Keisuke knew his brother was visiting Professor Hideto Miyajima near Mount Fuji and drove to his laboratory. Along the way, Keisuke witnessed Godzilla battle Anguirus, remarking that it didn't seem right for Anguirus to attack his friend Godzilla. After the battle, Keisuke recovered a chunk of strange metal where Godzilla had been standing. Keisuke brought it to Miyajima's laboratory, where the professor confirmed it to be identical to a piece of metal recovered by Masahiko in Gyokusen Cave. Miyajima said that this metal was "Space Titanium," a metal that could not be found anywhere on Earth. Miyajima said he wanted to get a closer look at Godzilla, and traveled to Tokyo with his daughter, Keisuke, and Masahiko. There, they witnessed a second Godzilla appear and attack the other one. During the battle, Miyajima determined that the Godzilla that had emerged from Mount Fuji was a cyborg, a MechaGodzilla. MechaGodzilla then shed its disguise and revealed its true robotic form, battling Godzilla and knocking him into Tokyo Bay. MechaGodzilla then flew away to undergo repairs. Miyajima said he was certain that MechaGodzilla was being remotely controlled by aliens, possibly from Gyokusen Cave. Miyajima, his daughter, and Masahiko flew to Okinawa to investigate, while Keisuke and Saeko traveled there with the statue on a cruise ship called the Queen Coral, hoping to avoid being caught by the aliens.
On the ship, Keisuke told Saeko he felt like they were being watched. His paranoia only increased when he saw the strange man from the plane on deck. One morning, Yanagawa stole the statue from Saeko's cabin, but found Keisuke waiting for him. The two struggled, but Keisuke grabbed a pistol and fired it at Yanagawa, grazing his face. However, to Keisuke's shock, the bullet wound revealed a green ape-like face underneath Yanagawa's skin. Yanagawa panicked and grabbed the statue, then ran on deck. Keisuke chased Yanagawa but lost sight of him. Yanagawa jumped onto Keisuke and held him at gunpoint. Before Keizuke could be killed, Yanagawa was shot in the back and fell overboard with the statue. Saeko ran to Keisuke and told him the statue was gone. Keisuke replied that he knew and told Saeko what happened. Keisuke remarked that he was worried about how Yanagawa fell, it was like he had been shot by someone. When the Queen Coral arrived in Okinawa, the ship's captain gave Keisuke another statue, much to Saeko's surprise. Keisuke revealed that the statue in Saeko's cabin had been a decoy, and that he had given the real statue to the captain to be securely hidden, claiming that "What friends don't know, enemies won't know."
When Keisuke and Saeko arrived at the hotel where Miyajima and the others were staying, the desk clerk revealed that they had never checked in. Saeko stayed behind with the statue while Keisuke went to Gyokusen Cave to look for them. In the cave, Keisuke was ambushed by an armed man, but was saved by the mysterious man he saw on the plane and the ship. The man introduced himself as Nanbara, an agent of Interpol. Nanbara said that he had been investigating the aliens for months, but he had been following Keisuke ever since he became involved. Keisuke concluded that Nanbara had shot and killed Yanagawa on the ship, and thanked him for saving his life twice. Keisuke and Nanbara infiltrated the aliens' hidden base in the cave and rescued Miyajima and the others, who were about to be executed. They all escaped the base and prepared to leave in Keisuke's car, but Nanbara anticipated that the vehicle had been rigged with a bomb, and tripped it before anyone got into the car. Nanbara, Masahiko, and Miyajima decided to go back inside and deal with the aliens, while Keisuke and the others met up with Saeko to use the statue to awaken King Caesar. Before they could activate the statue, they were ambushed by two aliens, who were holding the Azumi princess Nami and her grandfather prisoner. Thankfully, Nanbara's partner Tamura saved them, and the statue was placed on a pedestal. When the sun rose, the statue fired a beam at a nearby cliff, revealing the sleeping King Caesar. Nami awakened the beast with a song, just before MechaGodzilla arrived. Godzilla arrived shortly afterward and together the two monsters defeated MechaGodzilla. Meanwhile, Miyajima and the others killed the aliens' leader Kuronuma and destroyed their base. Keisuke was present with everyone else when King Caesar's statue was placed in an alcove at the Azumi castle.