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.
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.
L'agence crypto-zoologique Monarch déploie de nombreux moyens pour combattre des créatures de tailles divines. Godzilla va affronter le papillon géant Mothra, le ptérosaure super-rapide Rodan, ainsi que son pire ennemi, le dragon King Ghidorah. Ces anciennes superespèces veulent toutes la suprématie et mettent en danger la survie de l'humanité. Mais laquelle d'entre elles va connaître la victoire sur les autres ?
Le retour de Godzilla dans une nouvelle aventure, qui menace le Japon, trois personnages uniront leurs forces pour tenter de l’arrêter. Dans ce nouveau film, Godzilla mesure 118 m de haut (dépassant ainsi le Godzilla de Gareth Edwards qui avait déjà des mensurations très respectables : 108 m de haut), la plus grande incarnation du personnage selon la Toho. Pour Hideaki Anno, l'ambition est de réaliser, selon ses termes "le plus terrifiant Godzilla jamais vu", le film mélangerait les techniques traditionnelles de costumes, et des effets 3D.
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.
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.
In 1992, journalist Kenichiro Terasawa (Kosuke Toyohara) is writing a book about Godzilla and learns about a group of Japanese soldiers stationed on Lagos Island in the South Pacific during World War II. They were unintentionally saved from a group of American soldiers by a mysterious dinosaur known as "Godzillasaurus" in February 1944. In 1954, the island was destroyed by a hydrogen bomb test and the radiation from the bomb mutated the dinosaur into Godzilla.
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.
The prologue of the film acknowledges the events of the first Godzilla film, while inventing its own timeline, explaining that the capital of Japan was moved from Tokyo to Osaka. The film takes place in an alternate universe with advanced technology, explaining that in 1966, Godzilla attacks the first Japanese nuclear plant in Tokai, Ibaraki Prefecture. After this, a section of Japanese Self Defence Force was dedicated to fight Godzilla, and was called G-Graspers. In 1996, clean plasma energy replaced nuclear energy, however this did not deter Godzilla from attacking. Plasma energy is also banned, due to the fact that Godzilla attacked the original plasma energy reactor.
In the aftermath of Godzilla's attack on Tokyo and his later imprisonment at Mt. Mihara. a team of scientists discovers cells left in the rubble by the monster and collects them. A group of American militants takes a sample of their own. They attempt to escape with them, but are killed by a lone assassin codenamed SSS9, who steals the sample and departs. He boards a cruise liner and heads to the Republic of Saradia to deliver the cells to the Saradia Institute of Technology and Science. The president of the institute wants to use the cells to merge with genetically modified plants, hoping to transform Saradia's deserts to vast greenery and end the country's dependence on oil wells for wealth. Dr. Genshiro Shiragami and his daughter, Erika, are enlisted to aid with the ambitious project. However, a terrorist bombing destroys the institute's laboratory, ruining the cells and killing Erika.