In the aftermath of Godzilla's attack on Tokyo and its later imprisonment at Mt. Mihara, the monster's cells are delivered to the Saradia Institute of Technology and Science, where they are to be merged with genetically modified plants in the hope of transforming Saradia's deserts into fertile land and ending the country's economic dependence on oil wells. Dr. Genshiro Shiragami and his daughter, Erika, are enlisted to aid with the project. However, a terrorist bombing destroys the institute's laboratory, ruining the cells and killing Erika. Five years later, Shiragami has returned to Japan and merged some of Erika's cells with those of a rose in an attempt to preserve her soul. Scientist Kazuhito Kirishima and Lieutenant Goro Gondo of the JSDF are using the Godzilla cells they collected to create "Anti-Nuclear Energy Bacteria", hoping it can serve as a weapon against Godzilla should it return. They attempt to recruit Shiragami to aid them, but are rebuffed. International tensions increase over the Godzilla cells, as they are coveted by both the Saradia Institute of Technology and Science and the American Bio-Major organization. An explosion from Mt. Mihara causes tremors across the area, including Shiragami's home, badly damaging the roses. Shiragami agrees to join the JSDF's effort and is given access to the Godzilla cells, which he secretly merges with one of the roses. A night later, rival Bio-Major and Saradian agents break into Shiragami's lab, but are attacked by a large plant-like creature which later escapes to Lake Ashino and is named "Biollante" by Shiragami. Bio-Major agents plant explosives around Mt. Mihara and issue an ultimatum to the Diet of Japan, warning that the explosives will be detonated and thus free Godzilla if the cells aren't handed over. Kirishima and Gondo attempt to trade, but Saradian agent SSS9 thwarts the attempt and escapes with the cells. The explosives go off, and Godzilla escapes. It attempts to reach the nearest power plant to replenish its supply of nuclear energy, but Biollante calls out to it. Godzilla arrives at the lake to engage Biollante in a vicious battle, and emerges as the victor. Godzilla proceeds toward the power plant at Tsuruga, but psychic Miki Saegusa uses her powers to divert it toward Osaka instead. A team led by Gondo meet Godzilla at the central district and fire rockets infused with the anti-nuclear bacteria into its body. Gondo is killed in the process, and an unaffected Godzilla leaves the city. Kirishima recovers the cells and returns them to the JSDF. Shiragami theorizes that if Godzilla's body temperature is increased, the bacteria should work against it. The JSDF erects microwave-emitting plates during an artificial thunderstorm, hitting Godzilla with lightning and heating up its body temperature during a battle in the mountains outside Osaka. Godzilla is only moderately affected, but Biollante arrives to engage it in battle once again. The fight ends after Godzilla fires its atomic heat ray inside Biollante's mouth. An exhausted Godzilla collapses on the beach, and Biollante disintegrates into the sky, forming an image of Erika amongst the stars. Shiragami, watching the scene, is killed by SSS9. Kirishima chases the assassin and, after a brief scuffle, SSS9 is killed by a microwave-emitting plate. The sea water having cooled it and so stopped the bacteria, Godzilla reawakens and leaves for the ocean.