Shortly after his election as the first Japanese Secretary-General of the UN, Naotaro Daigo was interviewed by Nitto Television journalist Anna Otonashi, explaining that he believed the United Nations must help mankind in realizing its potential. Later, Daigo boarded a plane to New York City to give a conference. As his assistant brought him his notes, he stopped dead in his tracks as he looked out the airplane window. The monster Rodan suddenly swooped past, triggering a shockwave which caused the plane to explode. Daigo seemed to disappear in the crash, his whereabouts left unknown.
Following a series of monster attacks at key locations across the globe, fleets of UFOs seemingly eliminated them. A giant mothership appeared over the Earth Defense Force headquarters, and soldiers took position on the rooftop of the facility, prepared to open fire. Suddenly, a beam of light shone down from the craft, revealing none other than Naotaro Daigo, who explained to EDF Commander Reiko Namikawa and Major General Kunikida that he had been rescued by a peaceful race of aliens. The mothership beamed the three onboard, where they were met by the Xilien Commander and Staff Officer, who explained that they were a neutral race seeking only friendship with humanity. They continued that a rogue planet called Gorath was on an imminent collision course with the Earth, and that if all available firepower could not be concentrated on the planet it would spell the extinction of life as we know it.
Daigo organized a press conference to announce the launch of the "Space Nations," an alliance between the United Nations and the Xiliens. However, Otonashi, who had attended the conference, began to become suspicious of Daigo. After consulting tapes of Daigo's talk with her sister Miyuki and EDF Ensign Shinichi Ozaki, she realized that Daigo never blinked—as if he was not truly human. Her suspicions were confirmed when, after a mysterious assassin managed to stab Daigo in the hand, a sample of his blood proved him to be not of this Earth: an Xilien imposter who had assumed the Secretary's identity. As Daigo held another Space Nations conference, this time joined by the Xilien leaders, Miyuki sneaked into the EDF's data room to access confidential information on Daigo. However, she was soon confronted by two more imposters who had taken the forms of Namikawa and Kunikida. As it would turn out, the operation was actually a set-up to reveal the true identities of the masquerading aliens. After letting their true colors show, the two were gunned down by Captain Douglas Gordon and a group of Mutants who were standing by. Meanwhile at the conference, Anna told Daigo she had a surprise for him, and brought a dog onstage to the Secretary-General's confusion. Otonashi urged Daigo to call the dog's name, but he seemed unable to remember it; after she revealed its name to be Clint, the man pretended as if he knew it all along. Otonashi then revealed that it wasn't his dog at all, and he therefore could not have known its name, exposing him as an imposter on live television.
Gordon then crashed the conference holding the corpse of one of the other Xilien imposters, which he threw onstage in view of the cameras. He shot the false Daigo in the chest, causing him to begin bleeding profusely from the mouth and reverting violently into his true form. With the aliens' plans unraveling, the Xilien Staff Officer assassinated his superior, usurping his role as Commander and taking control of the invasion force. This culminated with him unleashing the monsters that had previously attacked, which were in fact under the Xiliens' control all along. Gordon launched a plan to use the battleship Gotengo to free Godzilla from the South Pole, believing him to be their last chance at survival. After leading Godzilla across the globe, picking off the aliens' pawns one by one, the Gotengo returned to Japan and pierced the Xilien Mothership's defenses, drilling itself into the ship's hull. The Gotengo's passengers were intercepted by the Xiliens, who killed most of its crew and brought the remainder onboard. A fight eventually broke out on the command deck, and was joined in on by the real Daigo, Namikawa and Kunikida who managed to escape their imprisonment. The group fought through Xilien forces as Ozaki was left to deal with the Controller. They eventually managed to escape back to the Gotengo just before the Mothership was destroyed, and after Ozaki aided Godzilla in defeating the aliens' ultimate weapon Keizer Ghidorah, the King of the Monsters shot the Gotengo down, but spared its passengers at the insistence of Minilla. As Godzilla and Minilla departed into the sunset, Daigo and the others stood among the wreckage of what was once Tokyo, left to rebuild society.
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