The opening credits scroll over an animated image of the character Bambi serenely grazing while the Call to the Dairy Cows from Rossini's opera William Tell (1829) plays in the background. After the credits, Bambi looks up to see Godzilla's giant foot coming down, squashing him flat (set to the final chord of The Beatles' "A Day in the Life" played at half-speed). After a moment, the closing credits scroll over the image of Godzilla's foot on top of a squished Bambi. At the very end, Godzilla's claws twitch once.
After Yata (Toru Ibuki) is lost at sea, his brother Ryota (Toru Watanabe) steals a yacht with his two friends and a bank robber, the crew runs afoul of the giant lobster Ebirah, and washes up on the shore of an island, where a terrorist organization manufactures heavy water for their purposes, as well as a chemical that keeps Ebirah at bay. The organization, known as the Red Bamboo, has enslaved natives from Infant Island to help them, but the natives hope to awaken Mothra (now a full-grown moth metamorphosed from the larva that appeared in Ghidorah, the Three-Headed Monster) to rescue them.
Police Detective Shindo (Yosuke Natsuki) is assigned to guard Princess Selina Salno of Selgina (Akiko Wakabayashi) during the Princess' visit to Japan, due to a suspected assassination plot. Although Shindo is smitten with Selina's photograph, her plane never makes it to Japan, as it is destroyed by a bomb en route. At exactly the same time a meteorite shower draws the attention of Professor Murai (Hiroshi Koizumi), who along with his team of scientists strikes out into the wilderness to examine the largest of the meteors, which has magnetic properties.
When the Japanese freighter Eiko-maru is destroyed near Odo Island, the Bingo-maru is sent to investigate, only to meet the same fate with few survivors. A fishing boat from Odo is also destroyed, with one survivor. Fishing catches mysteriously drop to zero, blamed by an elder on the ancient sea creature known as "Godzilla". Reporters arrive on Odo Island to further investigate. A villager tells one of the reporters that "something large is going crazy down there" ruining the fishing. That evening, a ritual dance to appease Godzilla is held during which the reporter learns that the locals used to sacrifice young girls. That night, a large storm strikes the island, destroying the reporters' helicopter, and an unseen force destroys 17 homes, kills nine persons and 20 of the villagers' livestock.
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.
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.
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.
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.
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.
Giant insectoid aliens from a dying planet in "Space Hunter Nebula-M" plot to colonize the Earth. The aliens assume the forms of dead humans and work as the development staff of the peace-themed theme park, World Children's Land, the centerpiece of which is "Godzilla Tower". The Nebula-M aliens plan to use the space monsters Gigan and King Ghidorah, guided by two "Action Signal Tapes," to wipe out human civilization.
The microscopic alien lifeform Hedorah feeds on Earth's pollution and grows into a poisonous, acid-secreting sea monster. After it sinks an oil tanker and attacks Dr. Toru Yano and his young son Ken Yano, scarring them both, Hedorah's toxic existence is revealed to the public. Ken Yano has visions of Godzilla fighting the world's pollution, and insists Godzilla will come to humankind's aid against Hedorah.
Strange events are taking place in Okinawa. An Azumi priestess has a terrifying vision of a city being destroyed by a giant monster. A type of metal not found on earth is discovered in a cave by a spelunker, Masahiko Shimizu, who takes it to Professor Miyajima for examination. An excavation led by Masahiko's brother Keisuke accidentally uncovers a chamber filled with ancient artifacts and a mural bearing an ominous prophecy: "When a black mountain appears above the clouds, a huge monster will arise and try to destroy the world; but then, when the red moon sets and the sun rises in the west, two more shall appear to save humanity." Keisuke is joined by archaeologist Saeko Kaneshiro, who translates the prophecy and takes one of the artefacts, bearing the likeness of the legendary monster King Caesar, to study. Two men stalk them, one who speaks to them and claims to be a reporter interested in the story, the other of whom attempts to steal the statue from them but fails and flees.
In the year 1973, the most recent underground nuclear test, set off near the Aleutians, sends shockwaves as far south as Monster Island, disturbing the monsters, causing Anguirus to fall into a fault opened up by the consequential earthquakes and Rodan to fly off, while Godzilla decides to stay put.
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.