Gamera self-destructed to destroy several Gyaos in 1973, the tale picks up thirty three years later, when the son of one of the survivors of that incident finds an unusual egg, from which a baby turtle hatches. The boy, Toru, raises the creature, quickly realizing it as remarkable in that it hovers and breathes fire. The creature quickly outgrows the house, is relocated by Toru and his friends to maintain secrecy, and then disappears.
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.
In the 1960s, two astronauts, Fuji and Glenn, are sent to investigate the surface of the mysterious "Planet X". There they encounter advanced and seemingly benevolent human-like beings called the Xiliens and their leader The Controller. The aliens usher the astronauts into their underground base, and moments later the surface is attacked by a creature the Xiliens call "Monster Zero", but which the astronauts recognize as King Ghidorah, a planet-destroying monster that had attacked Earth once before. The monster eventually leaves, but the Controller states that Ghidorah has been attacking repeatedly, forcing them to live underground in constant fear. He requests to borrow the Earth monsters Godzilla and Rodan to act as sentries against Ghidorah's attacks, in return for the cure for cancer (the English dub says the formula can cure any disease). The astronauts return to Earth and deliver the message.
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.
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.
A team of scientists are trying to perfect a weather-controlling system. Their efforts are hampered by the arrival of a nosy reporter and by the sudden presence of 2-meter tall giant praying mantises. The first test of the weather control system goes awry when the remote control for a radioactive balloon is jammed by an unexplained signal coming from the center of the island. The balloon detonates prematurely, creating a radioactive storm that causes the giant mantises to grow to enormous sizes. Investigating the mantises, which are named Kamacuras (Gimantis in the English-dubbed version), the scientists find the monstrous insects digging an egg out from under a pile of earth. The egg hatches, revealing a baby Godzilla. The scientists realize that the baby's telepathic cries for help were the cause of the interference that ruined their experiment. Shortly afterwards, Godzilla arrives on the island in response to the infant's cries, demolishing the scientist's base while rushing to defend the baby. Godzilla kills two of the Kamacuras during the battle while one manages to fly away to safety, Godzilla then adopts the baby.
Ichiro Miki (Tomonori Yazaki) is a highly imaginative but lonely latchkey kid growing up in urban (and at that time, polluted) Kawasaki. Every day he comes home to his family's empty apartment. His only friends are a toymaker named Shinpei Inami (Eisei Amamoto) and a young girl named Sachiko (Hidemi Ito). Every day after school, Ichiro is tormented by a gang of bullies led by a child named Sanko Gabara (Junichi Ito). To escape his loneliness, Ichiro sleeps and dreams about visiting Monster Island. During his visit he witnesses Godzilla battle three Kamacuras and Ebirah, a giant sea monster. Ichiro is then chased by a rogue Kamacuras and falls into a deep cave, but luckily avoids being caught by Kamacuras. Shortly afterwards, Ichiro is rescued from the cave by Godzilla's Son, Minilla. Ichiro quickly learns that Minilla has bully problems too, as he is bullied by a monstrous ogre known as Gabara.
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.
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.
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.
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.