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.
Far north of the Arctic Circle, a nuclear bomb test, dubbed "Operation Experiment", is conducted. Prophetically, right after the blast, physicist Thomas Nesbitt (Paul Christian) muses, "What the cumulative effects of all these atomic explosions and tests will be, only time will tell." No sooner said, the explosion awakens a 30-foot (10 m) tall, 100-foot (30 m) long carnivorous animal known as Rhedosaurus, thawing it out of the ice where it had been held in suspended animation. Nesbitt is the only witness to the beast's awakening and is later dismissed out-of-hand as being delirious at the time of his "sighting". Despite the skepticism he persists, knowing what he saw.
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.
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.
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.
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.
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.
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.
News reporter Ichiro Sakai and photographer Junko Nakanishi take pictures of a wreckage caused by a typhoon. They uncover a strange, bluish-gray object in the debris, not knowing its significance. Later that day, a giant egg is discovered on the shore. The local villagers salvage it, and an entrepreneur of Happy Enterprises named Kumayama buys the egg from the local villagers. Instead of letting scientists study the egg, Kumayama wants to make it into a large tourist attraction. Later, Sakai and Nakanishi are informed that the strange object they found is extremely radioactive. (It is later hinted that this is a skin particle from Godzilla.
Four years after the disaster at Jurassic Park, the wealthy Bowman family makes an excursion to the island of Isla Sorna during a yachting cruise. Their young daughter wanders off and is attacked by a pack of Compsognathus, but survives. The incident allows Peter Ludlow, John Hammond's nephew, to gain control of his uncle's company InGen, which is in severe financial straits after the events at Jurassic Park. Hammond contacts Ian Malcolm and explains that Isla Sorna is the island where the dinosaurs were engineered and nurtured before being moved to Isla Nublar, Jurassic Park's location. He also explains that after the park was shut down, Isla Sorna was abandoned during a hurricane and the dinosaurs left to survive in the wild, where they have been inexplicably thriving. Hammond asks Malcolm to join a team that will travel to Isla Sorna to document the dinosaurs in order to rally public support against human interference on the island. Ian initially declines but, after learning that his girlfriend, paleontologist Sarah Harding, is part of the team and is already on the island, he agrees to go.
While Scrat inadvertently causes the break up of Pangaea, Manny and Ellie are forced to deal with the trials and tribulations of their teenage daughter Peaches, who has trouble fitting in with her peers. Ellie tries to support her daughter, but Manny becomes exceedingly over-protective. Peaches' friend Louis, a molehog, tries to warn her as she tries to approach a mammoth named Ethan on whom she has a crush. Meanwhile, Sid's family returns, but only long enough to drop off the elderly Granny before abandoning them both. Manny catches Peaches sneaking off to meet Ethan, and leading to an argument and their estrangement. Shortly after, a continental break-up separates Manny from the herd. Trapped on a moving chunk of ice with Sid, Granny, and Diego, Manny has no choice but to ride out the current. Meanwhile, a giant land shift encroaches on Ellie, Peaches, and those remaining on land, causing them to make their way toward the land bridge.
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.
During the end of the Cretaceous era, an Iguanodon mother is forced to abandon her nest during a Carnotaurus attack. The one surviving egg journeys through several predicaments, before ending up on lemur island, where Plio names the hatched baby Aladar and raises him. Years later, Aladar and the lemurs take part in a mating season, where Zini goes without a mate. After the season ends, a meteor strikes and destroys the island, leaving Aladar, Plio, Yar, Zini and Suri, as the only survivors when they swim to the mainland. The family mourns for the loss of all lemurs before moving on.
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.