An expedition to an irradiated island brings civilization in contact with a primitive native culture. When one sensationalist entrepreneur tries to exploit the islanders, their ancient deity arises in retaliation.
New Mexico State Police troopers Ben Peterson (James Whitmore) and Ed Blackburn (Chris Drake) discover a little girl in shock, wandering the desert near Alamogordo, New Mexico. They retrace her steps to a mobile home owned by an FBI agent named Ellinson, who was on vacation in the area with his family. The side of the trailer was ripped open from the outside, the rest of the family is missing and no money was taken. A single unidentifiable animal track seems to be the only clue. Then a strange, pulsating high-pitched noise echos out of the desert on the wind. The little girl briefly reacts in fear when she hears the sound, but this is not noticed by those around her.
At University of Zurich Institute of Medicine in Switzerland, Herbert West brings his dead professor, Dr. Hans Gruber, back to life. There are horrific side-effects, however; as West explains, the dosage was too large. When accused of killing Gruber, West counters: "I gave him life!"
American reporter, Steve Martin (Raymond Burr), is brought to a hospital with dozens of maimed and wounded citizens. In flashback, Martin recalls stopping over in Tokyo, where a series of ship disasters catches his attention. When a survivor finally washes up on Odo Island, Martin flies there for the story with Tomo Iwanaga (Frank Iwanaga), a representative of the Japanese security forces and learns of the island inhabitants' belief in a sea monster god known to them as "Godzilla", which they believe is causing the disasters.
Two pilots named Shoichi Tsukioka and Koji Kobayashi are hunting for schools of fish for a tuna cannery company in Osaka. Kobayashi's plane malfunctions and is forced to land near Iwato Island, an uninhabited strip of rocks formed by volcanic eruptions. Tsukioka then looks for Kobayashi and finds him safe, with only a wrist sprain. While talking, the two men hear some strange sounds and find two monsters fighting. Tsukioka immediately recognizes one of the monsters to be Godzilla. The two monsters then fall off a cliff, into the ocean.
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.
A nuclear submarine on maneuvers in the Pacific Ocean, captained by Commander Pete Mathews (Kenneth Tobey), comes into contact with a massive sonar contact. The boat is disabled but manages to free itself and return to Pearl Harbor. Animal tissue of great proportions is discovered jammed in its dive planes. A man-and-woman team of marine biologists, Lesley Joyce (Faith Domergue) and John Carter (Donald Curtis), is called in; they identify the tissue as being part of a gigantic octopus. The military authorities scoff, but are finally persuaded after receiving reports of missing swimmers and ships at sea being pulled under by a large animal. Both scientists conclude the sea beast is from the Mindanao Deep, having been forced from its natural habitat by hydrogen bomb testing in the area, which has made the giant creature radioactive, driving off its natural food supply.
At the close of the 20th century, all of the Earth's kaiju have been collected by the United Nations Science Committee and confined in an area known as Monsterland, located in the Ogasawara island chain. A special control center is constructed underneath the island to ensure that the monsters stay secure, and to serve as a research facility to study them.
In the small mining village of Kitamatsu, on the southern Japanese island of Kyushu, two miners have gone missing. The two men, Goro and Yoshi, had brawled earlier that day, and after they entered the mine to start their shift, the shaft had quickly flooded. Shigeru Kawamura (Kenji Sahara), a tunneling and safety engineer at the mine, heads below to investigate and makes a gruesome discovery: Yoshi's lacerated corpse. Above ground, a doctor examines Yoshi, and discovers the cause of death to be a series of deep gashes caused by an abnormally sharp object. Some of the miners and their families begin to discuss the possibility of the involvement of Goro, who is still unaccounted for, in the death. Shigeru is personally affected by this incident, since his fiancée Kiyo (Yumi Shirakawa) is also Goro's sister.
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.
At Dark Waters, a Native American sacred land containing an enigmatic swamp spirit, a teenager is murdered by a plant-like monster. The following day, young replacement sheriff Kyle Williams reaches Bywater and meets with deputy sheriff Fraser, who tells him the previous sheriff is among 47 missing persons since oil tycoon Fred Schist bought the ancient tribal lands from shaman and Seminole chieftain Ted Sallis, the first to disappear. Schist claimed Sallis had sold legally and escaped with the money, and asked the sheriff for help: Local protestors opposed his perfectly legal activities, and mestizo scoundrel Renee Laroque was sabotaging his facilities. Williams investigated this while trying to find an explanation for the missing people, some of which were found brutally murdered with plants growing from inside their bodies. Photographer Mike Ploog and shaman Pete Horn tell Williams local legends about the guardian spirit, suggesting that it could be real.
A plane crashes on an island, and the pilot comes across a giant spider, which kills both him and an alien. One year later, Mercer (Alex Reid), the sister of the pilot, accompanies Valentine (Chris Potter) to the same island to locate her brother. On the way to a native village to examine several natives who are dying of spider bites, ticks burrow into Reyes (Luis Lorenzo Crespo). Upon reaching the village, they discover that the village has moved on. Reyes begins to cough up the ticks and Bear (Rocqueford Allen) decides to shoot him to end his suffering.
A man with Neanderthal features and wearing pajamas stumbles through the Arizona desert, falls and dies. Dr. Matt Hastings (John Agar), a bright, handsome and sympathetic doctor from the small town of Desert Rock, is called to view the body. Asked to give an opinion as to cause of death, he finds himself perplexed. Surprised to learn the deceased was someone he knew – biological research scientist Eric Jacobs – Dr. Hastings suggests he be given permission to perform an autopsy to learn why the man's face is distorted beyond recognition. The sheriff refuses, judging an autopsy unnecessary as Jacobs' associate, Dr. Gerald Deemer (Leo G. Carroll), signed the death certificate and there is no indication of foul play.
A group of scientists land on a remote island in the Pacific Ocean to search for the previous expedition that disappeared without a trace and to continue their research on the effects of radiation from the Bikini Atoll nuclear tests on the island's plant and sea life. They learn to their horror that the earlier group have been killed and eaten by two mutated, intelligent giant crabs, who have also absorbed the minds of their victims and can speak telepathically in the voices of their victims.
Captain Thorne Sherman and first mate Rook Griswold deliver supplies by boat to a group on a remote island. The group, consisting of scientist Marlowe Cragis, his research assistant Radford Baines, the scientist's daughter Ann, her recent fiancé Jerry Farrel, and a servant Mario, welcome the captain and his first mate, but subtly resist the visitors staying overnight, even though a hurricane approaches. Thorne goes with the group to their compound. Griswold stays with the boat, to come ashore later.