In 1954, a nuclear bomb is detonated at the moment a giant creature emerges from the ocean. In 1999, Project Monarch scientists Ishiro Serizawa and Vivienne Graham investigate a colossal skeleton unearthed in a collapsed mine in the Philippines. They find two spores; one dormant and one hatched that made a trail into the sea. In Japan, the Janjira Nuclear Power Plant experiences unusual seismic activity and Supervisor Joe Brody sends his wife Sandra and a team of technicians into the reactor. A tremor breaches the reactor, leaving Sandra and her team unable to escape while the plant collapses.
L'agence crypto-zoologique Monarch déploie de nombreux moyens pour combattre des créatures de tailles divines, appelées Titans. Ces derniers réapparaissent petit à petit des entrailles de la terre. La paléobiologiste Emma Russell, travaillant pour Monarch, a été traumatisée par la mort de son fils Andrew en 2014. Elle a mis au point l'Orca, jadis imaginé avec son ex-mari Mark, une machine qui permet de capter et reproduire les signaux émis par les Titans. Son invention attire des convoitises. Emma entraine avec elle sa fille Madison. Son père, Mark va tout faire pour retrouver sa fille, tout en tentant de survivre dans un monde envahi de monstres. Godzilla va ainsi devoir compter sur une alliée, le papillon géant Mothra pour affronter les 2 menaces que représentent le ptérosaure super-rapide Rodan, ainsi que son pire ennemi, le dragon à trois têtes King Ghidorah, qui est l'Alpha des Titans. Ces anciennes super-espèces veulent toutes la suprématie et mettent en danger la survie de l'humanité. Alors qu'un combat apocalyptique se prépare, Godzilla, seul prétendant au titre capable de rivaliser avec l'Alpha, aidé des humains, devra s'imposer et ainsi affirmer sa place en tant que roi des monstres.
Following a nuclear test in French Polynesia, the fallout irradiates a lizard's nest. Decades later, an enormous sea creature suddenly attacks a Japanese fishing vessel in the South Pacific, leaving only one fisherman alive. Dr. Niko "Nick" Tatopoulos, an NRC biologist, is sent to Tahiti and to Jamaica, where a wrecked village, footprints, and ship are found. Nick collects skin samples that lead him to believe the creature is an enormous mutant created by nuclear testing. It travels to New York City during the rainiest week of the season, leaving a path of destruction in its wake.
Une créature géante se manifeste dans la baie de Tokyo, avant de faire surface et de terroriser la ville. Le cabinet ministériel se réunit d'urgence, mais le Premier Ministre est incapable de prendre une décision. Les radiations mesurées sur le passage de la créature démontrent qu'elle est le triste produit d'une contamination. Plus tard, elle évolue et revient sous une forme encore plus monstrueuse, réduisant Tokyo en poussière. Devant l'ampleur de la menace, les États-Unis décident d'utiliser l'arme nucléaire sur le Japon si ce dernier échoue à éradiquer la menace, réveillant le spectre des bombardements d'Hiroshima et de Nagasaki. Une équipe de chercheurs se regroupe alors en marge des décisions du Cabinet pour déterminer comment éliminer le monstre, surnommé "Godzilla". La France et l'Allemagne finiront par s'en mêler à leur tours.
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.
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.
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.
Kiryu is undergoing repair modifications after its battle with Godzilla. Prime Minister Hayato Igarashi accepts Lead Scientist Yoshito Chujo's choice to replace the Absolute Zero Cannon with a powerful Tri-Maser.
Endless warfare and environmental pollution have resulted in the frequent appearance of monsters. The Earth Defense Force (EDF) is established. Mutant humans with extraordinary physical capabilities are discovered and are organized into an EDF troop called the M-Organization. Their main opponent is Godzilla, first sighted in 1954. After repeated battles, Godzilla is captured in a crevasse at the South Pole and buried under an avalanche of ice. The EDF ship Gotengo, commanded by Captain Gordon, battles and destroys Manda but in the process, the ship is wrecked and Gordon is dismissed from the EDF. At M headquarters, mutants Ozaki and Kazama spar before their next mission.