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Four years after Godzilla's rampage, a team of mercenaries from a corporation called Biomajor attacked a goverment team that was recovering the peices of Godzilla's flesh from the destroyed city. The mercanaries steal the G-cells but are caught and gunned down by an agent of the Middle Eastern country of Saradia. He steals them and uses them for his own country. The dictator of Saradia has built a lab for a Japanese Scientist named Dr. Shiragami. But a bomb from a terrorist strikes the lab destroying it. Five years later, Dr.Shiragami combined the DNA from his daughter's body to the DNA of a rose. He did this in hope of her soul living on in a rose. However, Biomajor spied on Shiragami . But Biomajor was being watched by a terrorist known as SSS9. Meanwhile, Miki Saegua (who is a phsycic) soon discovered that Godzilla was awake in the volcano. Though the goverment didn't beleive her at first, they detected movements in the volcano. Miki was right. So the goverment activates the Super-X2. Biomajor breaks into Shiragami's lab to steal the cells but is attacked by the mutated plant. After the attack, the plant known as Biollante moves to Lake Ashino. With the other two tries that failed, Biomajor threatens to activate the bombs they have placed on Mount Mihara thereby releasing Godzilla. The boverment attempts a trade but the terrorist SSS9 ruins the trade and Godzilla was released. The Super-X2 engages in a fight with Godzilla. But not even with the reflective barrier, the Super-X2 is forced to retreat. Godzilla soon arrived at Lake Ashino and fought Biollante. After a short fight, Biollante dissolves into golden spores and travels in the Earth's atmosphere. Godzilla heads toward Osaka. But while in Osaka, Godzilla is injected with Anti-Nuclear Energy Bacteria with is supposed to eat away a his nuclear energy. But the plan doesn't work. After Godzilla passes the JSDF and fights Biollante's final form. After Godzilla shot his Atomic ray in her mouth, she dissolves into spores and stays in the Earth's atmoshpere. Suddenly the ANEB takes effect and Godzilla' body temperature rises. Godzilla staggers toward the ocean. The cold water wakes him up as he walks home.