The film begins with a raid by the apelike Wagabu tribe on the early Homo sapiens Ulam tribe, who possess fire in the form of a carefully guarded small flame which they use to start larger bonfires. Obtained from a natural source, the flame is kept in a fabricated bone satchel and must be fed constantly to keep it alive, because the Ulam don't know how to start a fire. Driven out of their home after a bloody battle with the Wagabu, the surviving Ulam escape but are chased into a marsh by a pack of wolves. The Ulam's bald-headed fire tender escapes with the tribe's remaining fire; however, while crossing a marsh, he all but douses the embers, leaving the tribe doomed to die from exposure and starvation. The Ulam elder decides to send three men, Naoh (Everett McGill), Amoukar (Ron Perlman) and Gaw (Nameer El-Kadi), on a quest to find fire.
The film incorporates characters and events from several of the albums, in particular the first, "Adèle and the Beast," first published in 1976, and the fourth, 1978's "Mummies on Parade," within an overall plot of Besson's construction and takes place primarily in Paris, France, circa 1912.
Godzilla is a literal force of nature to Japan. The Godzilla Prediction Network (GPN) functions independently to study the monster and predict its landfalls. Meanwhile, the scientists of Crisis Control Intelligence (CCI) find a sixty million year old UFO deep in the Japan Trench. As CCI attempts to raise the UFO to study it, it takes off into the sky on its own. Godzilla arrives and battles the Japan Self Defense Forces, now equipped with powerful Full Metal Missiles, but the UFO appears, searching for genetic information that only Godzilla possesses. It defeats Godzilla, driving the monster underwater, and then lands to replenish its solar power.
Godzilla cells brought into space by Biollante and Mothra are exposed to intense radiation from a black hole. The celestial fission creates a highly aggressive extraterrestrial beast closely resembling Godzilla. This "SpaceGodzilla" quickly makes its way to Earth.
In 1993, an asteroid lands in the ocean and awakens Godzilla. The next day, a young man named Takuya Fujita is detained after stealing an ancient artifact. Later, a representative of the Japanese Prime Minister arrives with Takuya's ex-wife, Masako Tezuka, and offers him to explore an island with Masako and Marutomo company secretary, Kenji Ando, and become a free man. Takuya initially turns down the offer, on the basis that he is to be released in another week. But after his ex-wife informs him that his sentence has been reconsidered, he accepts. After the trio arrives at the island, they find a cave behind a waterfall. Inside, they discover ancient paintings, including a picture of two giant insects fighting one another. While studying them, the sun shines through a hole in the wall, and the light points to a small opening in the cave, where they come upon a giant egg. The three hear a pair of voices, which belong to the Cosmos. They keep the earth's natural order in balance, and informs them the egg belongs to Mothra.
During a meeting of the Japan Self-Defense Forces (JSDF) for the potential return of Godzilla, Admiral Taizo Tachibana briefs cadets about Godzilla's first attack. A nuclear submarine is reported missing, which is later found to have been destroyed by Godzilla. Tachibana's daughter, Yuri Tachibana films a docudrama with her crew at Mt. Myoko, where a mysterious earthquake randomly ensues. The odd earthquake returns later that night burying a biker gang and leaving one surviving trucker who witnesses the monster, Baragon.
In 1992, the United Nations establishes the United Nations Godzilla Countermeasures Center (UNGCC) to stop Godzilla. The remains of Mecha-King Ghidorah are salvaged from the ocean and used to create two anti-Godzilla machines. The first is a flying gunship called Garuda. The second and more powerful machine, modeled after Godzilla itself, is called Mechagodzilla.
In 1996, after the death of SpaceGodzilla, Miki Saegusa travels to Birth Island to check on Godzilla and its adopted child, but finds the entire island destroyed. Godzilla appears in Hong Kong, covered in glowing lava-like rashes. It goes on a rampage, causing major collateral damage and killing thousands of civilians. A group of representatives from the Japan Self Defense Forces (JSDF) hires college student Kenichi Yamane, the grandson of Dr. Kyohei Yamane, to work at the center in an attempt to unravel the mystery of Godzilla's condition. Yamane suspects that Godzilla's heart, which acts as a nuclear reactor, is going through a nuclear meltdown. He theorizes that, when Godzilla's temperature reaches 1,200 degrees Celsius, it will explode with a force approximately "1,000 times greater than all nuclear weapons put together, a burst of power unseen since time began.
A ship carrying plutonium collides with a floating atoll off the eastern coast of the Philippines, one of many incidents occurring throughout the area. As the anomalous formation approaches Japan, a team of scientists led by Naoya Kusanagi (Akira Onodera) discover orihalcum amulets and a stone slab covered in Etrurian runes on the atoll. During the investigation, the atoll suddenly quakes, destroying the slab and throwing the scientists into the ocean. One member of the team, Marine Officer Yoshinari Yonemori (Tsuyoshi Ihara), sees the eye and tusk of a giant turtle.
In 1999, 45 years after Godzilla's first attack, Lieutenant Akane Yashiro, a mazer-cannon technician, is unable to kill a new member of Godzilla's species during her first fight. She is made a scapegoat for the military's losses during the battle and transferred to a desk job. During the battle, it was discovered that Godzilla is immune to mazer fire, rendering all of the Japanese military useless against it should it return. Scientists, including single father Tokumitsu Yuhara, are gathered to build a bio-mechanical robot from the original Godzilla's skeleton. Four years later, the cyborg Mechagodzilla, named Kiryu, is finished and inducted into the Japan Self-Defense Forces along with its human pilots as the Kiryu Squadron. Akane becomes the main pilot for Kiryu. However, memories of Akane's actions during the original fight still linger, and one of her squadron mates, Second Lieutenant Susumu Hayama holds her responsible for the death of his brother.
Atouk (Starr) is a bullied and scrawny caveman living in "One Zillion BC – October 9th". He lusts after the beautiful but shallow Lana (Bach), who is the mate of Tonda (Matuszak), their tribe's physically imposing bullying leader. After being banished along with his friend Lar (Quaid), Atouk falls in with a band of assorted misfits, among them the comely Tala (Long) and the elderly blind man Gog (Gilford). The group has ongoing encounters with hungry dinosaurs, and rescues Lar from a "nearby ice age", where they encounter an abominable snowman. In the course of these adventures they discover sedative drugs, fire, invent cooking, music, weapons, and learn how to walk fully upright. Atouk uses these advancements to lead an attack on Tonda, overthrowing him and becoming the tribe's new leader. He rejects Lana and takes Tala as his mate, and they live happily ever after.
Three years have passed since Gamera defeated the Legion, and the world is once again plagued by the Gyaos, which have evolved into Hyper Gyaos. Mayumi Nagamine, noted ornithologist, returns to aid the Japanese government in addressing this threat. A graveyard of Gamera fossils is found at the bottom of the sea. Shadowy government agents, occultist Miss Asukura and Kurata Shinji, are meanwhile working to a different agenda, with Asukura believing Gamera to be an evil spirit.
George Loomis (William Katt) and and his wife Dr. Susan Matthews-Loomis (Sean Young) find a family of Mokele-mbembe (referred to as Brontosaurs) in Central Africa and they struggle to protect them from a greedy scientist named Dr. Eric Kiviat (Patrick McGoohan) and the military.
A year has passed since the battle between Gamera and the Gyaos, and Japan has struggled to rebuild its cities in the meantime. The military has kept a cautious vigil on the nation's coast, but so far Gamera has yet to return. Suddenly, a series of bizarre incidents reveal a new threat to the land of the rising sun. On a moonlit stroll, science instructor Midori Honami watches as a huge meteor plunges into the mountain snow. The next night, two security guards are horrified as they see large insect-like creatures stealing glass bottles from a nearby warehouse. Soon after, the entire city of Sapporo is covered with strange plants and the link between these events soon becomes clear.
Mr. Tako, head of Pacific Pharmaceuticals, is frustrated with the television shows his company is sponsoring and wants something to boost his ratings. When a doctor tells Tako about a giant monster he discovered on the small Faro Island, Tako believes that it would be a brilliant idea to use the monster to gain publicity. Tako immediately sends two men, Sakurai and Kinsaburo, to find and bring back the monster. Meanwhile, the American submarine Seahawk gets caught in an iceberg. The iceberg collapses, unleashing Godzilla (who, in the Japanese version, had been trapped within since 1955), who then destroys the submarine and a nearby military base.