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.
Suneo shows everyone but Nobita a fossil of dinosaur claw. Angry, Nobita claims he will be able to find a living dinosaur. As Doraemon refuses to help him, he digs on a hillside, but instead earns punishment from a landlord nearby who forces him to unearth a hole in the ground. He finds an egg-shaped stone underneath and quickly uses a time wrap to return it to its former form and after warming it, the egg hatches to reveal a Futabasaurus, who is subsequently named Piisuke by Nobita. Instead of immediately showing it to the others, Nobita waits it grow while making a deal with others. As Piisuke grows too large and is in danger of being found, Doraemon and Nobita transport him to 100 million years ago in the Late Cretaceous period. They are attacked by a mysterious assailant who previously tried to make a deal with Nobita to sell Piisuke, though they manage to escape. Left with no proof, Nobita instead shows them Piisuke through a television monitor, but realizes that he and Doraemon had unknowingly transported Piisuke to the North American shore after the time machine was attacked by the assailant. They and the others decide to go there, but the time machine is overloaded and crashes off.
Mario and Luigi are two Italian American plumbers living in Brooklyn, New York, who are currently being driven out of business by the mafia-like Scapelli Construction Company led by Anthony Scapelli. Later, Luigi falls in love with an orphaned NYU student named Daisy, who is digging under the Brooklyn Bridge for dinosaur bones. After a date, Daisy takes Luigi back to the bridge only to witness one of Scapelli's men sabotaging it by leaving the water pipes open. Unable to fix the flooding, Luigi and Daisy rush back to his apartment where they inform Mario about the incident. The trio returns to the flooding where the Mario Bros. manage to fix it but are knocked unconscious by Iggy and Spike, who proceed to capture Daisy.
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.
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.
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.
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.
Cody (Trevor Morgan), his sister Abby (Diana Rice), their best friend Marcella (Kyla Pratt), and their baby brother Fig are dropped off by their parents for a visit at their grandparents' farm. Cody gets hit in his face by a basketball by accident while Abby and Marcella laugh and rub a Barney doll in his face. Cody loses his patience and starts a game of "keep-away" by taking the Barney doll and runs off with it. The two girls go after Cody. He then hides the Barney doll in the shower in the bathroom and the girls catch up with him. Cody tells them to use their imagination and laughs when he thinks that it is not working. However, the doll comes to life and turns into Barney the purple dinosaur. Cody refuses to believe in Barney at first, claiming that imagination is just for kids and that "real dinosaurs don't talk and real dinosaurs don't laugh.