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In 1990, the J.S.D.F. with the assistance of the Okouchi Foundation began a project to genetically engineer a strain of bacteria capable of feeding on and breaking down nuclear materials, for the purposes of cleaning up fallout from any nuclear accidents in the country and potentially battling Godzilla if he ever emerged from Mount Mihara. The project was inspired by the successful breeding of bacteria that feed on oil to clean up oil spills in other countries. However, the bacteria required the genetic code to allow the production of an enzyme that breaks down nuclear materials into an edible form. The only known source of such a genetic structure was Godzilla's own cells, since his primary food source was nuclear energy. The Okouchi Foundation possessed the only known G-Cell samples in Japan, but there was no scientist capable enough to work with them. Scientist Kazuhito Kirishima, who was convinced to join the project to protect the country from Godzilla and prevent malevolent groups from producing the bacteria first, approached geneticist Genshiro Shiragami to ask for his help in breeding the bacteria. Shiragami refused at first, but changed his mind when an earthquake destroyed the rosebush containing the preserved cells of his deceased daughter, Erika. Shiragami accepted the job on the condition he could keep the G-Cells at his lab, secretly intending to splice them with a rose in order to keep it alive. Working with Kirishima, Shiragami successfully bred a strain of the ANEB, which began to multiply at a controlled rate. When the terrorist group Bio-Major learned of the breakthrough, it sent two agents, John Lee and Michael Low, to break into Shiragami's lab near Lake Ashi and retrieve his notes. Inside the lab, Lee discovered the notes on the ANEB, but he and Low were attacked by the Saradian agent SSS9, who had also come to steal the notes. Suddenly, the three were attacked by Biollante, the result of the G-Cells being spliced with the rose. Biollante killed Michael Low, but Lee and SSS9 escaped. The next day, Bio-Major planted explosives at Mount Mihara and threatened to detonate them and release Godzilla unless Japan handed over the ANEB to them. Kirishima and Colonel Goro Gondo brought a briefcase containing the ANEB to Mt. Mihara and handed it to John Lee, who allowed them to disarm the explosives from the back of his truck. Suddenly, SSS9 arrived and killed Lee by shooting him in the head with a sniper rifle, causing the truck to overturn. SSS9 retrieved the ANEB and retreated, while Kirishima and Gondo failed to disarm the explosives in time, releasing Godzilla.
SSS9 brought the ANEB to the Saradia Oil Corporation's office in Osaka, where it was prepared to be shipped back to Saradia. Gondo and Kirishima arrived at the office and knocked out the worker there, and took back the ANEB. Upon learning of this, Abdul Zaruman, the director of the Saradian Secret Service, ordered SSS9 to kill Shiragami and prevent Japan from ever producing the ANEB again. Back in Osaka, the ANEB was promptly weaponized and loaded into rockets wielded by an elite commando team led by Gondo. The commandos took point at the tops of several skyscrapers in the city center, while Sho Kuroki used the Super X2 to distract Godzilla. Godzilla destroyed the Super X2 and approached the city center, where Gondo fired multiple ANEB-loaded rockets at him. As Gondo prepared to leave, Godzilla approached a window and stared at him. Gondo responded by firing another rocket into Godzilla's mouth and taunted him, causing Godzilla to smash the building and kill Gondo. After several hours, Godzilla showed no ill effects from the ANEB as he continued his destructive trek across Japan. Kirishima realized that Godzilla's body temperature must have been too low for the ANEB to multiply, and proposed to the J.S.D.F. a plan to increase Godzilla's body temperature. The J.S.D.F. set up a field of experimental M6000 T.C. System devices and deployed several MBT-92 Maser Cannons near Wakasa Bay, where Godzilla was heading. The combined efforts of the Masers and the T.C. System successfully raised Godzilla's body temperature and he began to weaken. The operation was interrupted when Biollante arrived at the battlefield in her final form and attacked Godzilla. As the battle raged on, Godzilla's body temperature continued to rise and he became incredibly weak. Godzilla was forced to retreat, then suddenly fell headfirst to the ground in front of the ocean, seemingly dead. Biollante, seriously injured during the battle, retreated as well and floated up to space. Shiragami stated that Godzilla and Biollante were not real monsters, but the scientists who created them were. He vowed to end his work on Biollante and the ANEB for good. As Shiragami watched Biollante float up to space, he was shot and killed by SSS9. Kirishima chased after SSS9 and was ultimately overwhelmed and held at gunpoint, but was saved when Kuroki activated a T.C. pad and vaporized SSS9. Godzilla meanwhile had his body temperature lowered by the waves washing over his upper body, and rose back to his feet. Still weakened and infected by the ANEB, Godzilla waded out to the sea and disappeared.
Two years later, Godzilla was still infected by the ANEB and was forced to remain underwater at all times and hibernate frequently. He was being closely observed by the J.S.D.F., and had not moved very much over the last several weeks. A group of people from the 23rd century arrived in Japan and warned that Godzilla would eventually return and destroy the country, and proposed a plan to travel back in time to 1944 and remove the Godzillasaurus that would become Godzilla from Lagos Island before the hydrogen bomb test conducted at Bikini Atoll in 1954. The expedition arrived in 1944 and found the Godzillasaurus, then teleported it to the Bering Sea. Back in 1992, Godzilla had suddenly disappeared from the waters off Japan and was presumed to have been erased from existence. The Futurians meanwhile revealed their true colors, they were terrorists from the future who intended to equalize the world's economies and prevent Japan from becoming a global superpower by destroying it in the past using their monster King Ghidorah. Yasuaki Shindo, a Japanese businessman whose garrison had been saved by the Godzillasaurus during World War II, proposed a plan to find the dormant Godzillasaurus which was presumably in the Bering Sea and transform it into Godzilla by blasting it with nuclear torpedoes on-board his company's submarine so that he could defeat King Ghidorah. On the way to the Bering Sea, the submarine encountered the ANEB-infected Godzilla, who had never been erased from history at all. Godzilla destroyed the sub and fed on its nuclear energy, which completely cured his ANEB infection and caused him to grow from 80 to 100 meters in height.