One night in 1984, a fisherman out on a boat on Lake Ikeda notices the entire lake begin to glow brightly. At Kanoya Air Base, a JSDF Rear Admiral discusses recent rising radiation levels at Rolisican nuclear testing sites with his staff. He moves on to the next order of business, the strange glowing light reported by the fisherman. A Petty Officer jokes that the fisherman must have seen Issie, but the Admiral reminds him that monsters are very real as they learned less than a decade ago. He gives the order to plant depth charges in the lake, to the objections of photojournalist Mima Kinjo. The Admiral reminds her that she is a guest at the briefing and not a soldier, sailor, or scientist, and reiterates his order to destroy whatever is in the lake. Mima drives to Lake Ikeda and dons scuba gear to see what is under the lake. She finds Mothra, bound by chains marked "JSDF." She tries to cut them with a knife, but it breaks as her oxygen levels run out and she is forced to surface. Mima returns to her car and leaves to confront the Admiral about what she found. When Mima arrives at Kanoya Air Base, she finds the personnel scrambling in response to Godzilla being sighted off the coast of Yakushima. The Admiral briefs his men about Godzilla's impending attack and orders them to begin evacuations. Mima bursts into the briefing and suggests that Mothra could defeat Godzilla if she was freed. The Petty Officer is incredulous at the suggestion of unleashing another monster when one is already on its way, but the Admiral tells him to be quiet and dismisses him. The Admiral tells Mima she must have seen Mothra, and Mima responds by saying the Admiral knew what she was and decided to kill her the moment he thought he lost control of her. The Admiral responds that he would do it again, asking Mima where she was the last time Godzilla attacked. She replies that she was with her family at Ishigaki, and the Admiral says that she has no idea what these monsters can do and the destruction they can cause. He tells her to get herself as far away from the monsters as she can, but Mima purchases an underwater blowtorch and returns to Lake Ikeda to free Mothra. Once freed, Mothra bursts out of the lake and flies to the mainland to cocoon herself. Mima watches as Mothra flies away, but is caught by the JSDF and arrested.
After the release of 2004's Godzilla: Final Wars, marking the 50th anniversary of the Godzilla film franchise, Toho decided to put the series on hiatus for another 10 years. Toho also demolished the water stage on its lot used in numerous Godzilla, kaiju and tokusatsu films.[28] Yoshimitsu Banno, who had directed 1971's Godzilla vs. Hedorah, secured the rights from Toho to make an IMAX 3D short film production, based on a story similar to his Hedorah film. This project eventually led to the development of Legendary's Godzilla. Tsutomu Kitagawa portrayed Godzilla for the majority of the Millennium films, with the exception of Godzilla, Mothra and King Ghidorah: Giant Monsters All-Out Attack, in which Godzilla was portrayed by Mizuho Yoshida. Unlike the Shōwa and later Heisei films, the special effects for the Millennium films were directed by multiple effects directors such as Kenji Suzuki (Godzilla 2000, Godzilla vs. Megaguirus), Makoto Kamiya (Godzilla, Mothra and King Ghidorah: Giant Monsters All-Out Attack), Yuichi Kikuchi (Godzilla Against Mechagodzilla), and Eiichi Asada (Godzilla: Tokyo S.O.S., Godzilla: Final Wars).
The people of Japan soon learned that the Futurians had double-crossed them, with the three Dorats Emmy had left behind on Lagos Island having been exposed to the 1954 Castle Bravo H-bomb test and transformed into King Ghidorah. As King Ghidorah raided Fukuoka under the Futurians' command, Emmy suddenly grasped the horrific plans her colleagues had for Japan. She begged Wilson and Grenchiko to stop, but Grenchiko suggested that Emmy had seemingly forgotten their mission. Emmy replied that she had come back to warn Japan about its future, while Wilson and Grenchiko had resorted to terrorism to achieve their goals. Emmy stormed off and stole a BABY jetpack to find Terasawa and explain what was going on. Having seen Emmy leave, Wilson ordered M11 to follow her. Emmy flew BABY to Terasawa's house, where she came clean about who she was and why she had traveled back to 1992. The scenario the Futurians had laid out to the Japanese government was a fabrication. In reality, Godzilla never returned to menace Japan, allowing the nation to prosper. In the 23rd century, Emmy explained, Japan had become the world's leading economic superpower, which allowed it to purchase entire nations in Africa and South America. It was so powerful at this point that the Earth Union, the successor to the United Nations, was unable to control it or curtail its corrupt practices. Emmy belonged to a political organization known as the Equal Environment of Earth Union, or E3, which sought to equalize the power of all nations on Earth. Wilson, a more radical member of the organization, decided to take matters into his own hands and steal a time machine from the Earth Union and travel back to the past to prevent Japan from becoming a corrupt superpower in the first place. Emmy had accompanied him on the mission, but reneged once she learned what his methods were. While Emmy explained all of this to Terasawa, M11 spied on them from a distance. Emmy and Terasawa then met with Miki Saegusa, who remarked that she could clearly sense Godzilla moving through the ocean, as if he had never been erased from history at all. Emmy said it was possible that the dinosaur could have still become Godzilla through means other than nuclear testing, like if for example there had been nuclear waste where they had placed the dinosaur. Terasawa investigated news archives and learned that a Soviet nuclear submarine had sunk in the exact location where the dinosaur had been placed in the Bering Sea. He reported his findings to Emmy and Fujio, saying that Godzilla had not been erased from history at all and was instead created by this nuclear submarine crash. He expressed his intent to speak with the Japanese government before they tried to recreate Godzilla by irradiating the dinosaur they believed was still underwater using the Teiyo Group's nuclear submarine. Emmy insisted on accompanying him, but while they were driving they found themselves pursued by M11. Terasawa was able to evade M11's car, which crashed and exploded. However, M11 emerged from the burning wreckage and chased Terasawa and Emmy down on foot. He ran in front of Terasawa's car and stopped it with his bare hands. Terasawa prepared to get out of the car, but Emmy warned him that M11 would kill him. She said that M11 was here to take her back to the ship, and would leave Terasawa alone if she accompanied him. M11 brought Emmy back to Wilson and Grenchiko, who revealed that they knew about the government's plan to recreate Godzilla. While aboard MOTHER, Emmy reprogrammed M11 to be loyal to only her, and had him bring Terasawa aboard. There, they planned to sabotage Wilson and Grenchiko's plan by destroying the supercomputer they wanted to use to rebuild Japan to their liking.
As Godzilla rampaged through Shinjuku, Mecha-King Ghidorah appeared in the sky above. Piloted by Emmy and controlled by M11's computer, the cyborg touched down and began battling Godzilla. While at first Mecha-King Ghidorah was able to overpower Godzilla and bury him in rubble, Godzilla began blasting his foe with his atomic breath, damaging it. M11 told Emmy to make the cyborg fly, but as Mecha-King Ghidorah tried to fly away, Godzilla grabbed it by the legs. He fired his atomic breath at Mecha-King Ghidorah's wings, knocking it out of the sky and sending it crashing to the ground. As Emmy lay unconscious in the machine's cockpit, M11 yelled at her to get up and use the capture cables immediately. Emmy was able to regain consciousness and quickly pulled a lever that allowed Mecha-king Ghidorah to stand up and launch its electrified capture cables at Godzilla. M11 told Emmy to use the machine hand next, and she obliged, pressing a button that caused Mecha-King Ghidorah to launch a powerful metal claw that restrained Godzilla. As the cables and machine hand shocked Godzilla, Mecha-King Ghidorah took flight and began carrying Godzilla out over the ocean. M11 warned that Mecha-King Ghidorah couldn't take much more, only for Godzilla to fire a blast of atomic breath that caused both monsters to plummet into the sea below. As Terasawa and the others watched in shock, they were relieved to see KIDS fly out of the ocean safely. Terasawa and Miki thanked Emmy for saving Japan, with Terasawa expressing regret that he would have to live 200 years just to see her again. Emmy explained to Terasawa over a communicator that he was actually a distant grandfather of hers. M11 told Emmy that they would soon warp back to 2204, and before departing she bid farewell to her homeland.