While on a journey through the remote regions of the Amazon rainforest, a long extinct animal shot by Professor George Challenger's (Bob Hoskins) team turns out to be a prehistoric pterosaur. During a lecture at the Natural History Museum of London, he argues that it is genuine and that he shot it several months ago. The lecturer, Professor Leo Summerlee (James Fox) dismisses it as nothing more than a clever hoax, as do several others. Eventually ambitious Lord John Roxton (Tom Ward), a noted hunter and womanizer, and Daily Gazette columnist Edward Malone (Matthew Rhys) announce they will volunteer for the expedition and even Summerlee joins them.
In an alternate timeline in which Earth was never hit by an asteroid and dinosaurs never became extinct, a young Apatosaurus named Arlo loses his father in a tragic accident. One day, Arlo falls into a river and gets knocked out by a rock, finding himself far away from his home. While trying to find a way back to the Clawed-Tooth Mountains, he befriends a human caveboy that he names Spot.
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.
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.
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.
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.
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.
Stanley goes with his family and friend's to his great uncle's dude ranch. The local land baron is trying to buy the ranch and make it a parking lot for his nearby amusement park. The only way Uncle Stew thinks he can get any money to save his ranch is to find other dinosaur bones to attract customers. Stanley and his friends help in the search.
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.
The film begins on a summer's day in Northern Canada 70 million years ago and herd of Edmontosaurus and a spiky Edmontonia are feeding on the lush vegetation that grows all around them. Scar, a young male Edmontosaurus, enjoys his life in the Arctic forests with his extended family, comes across a young immature male Troodon named Patch, who has been feasting on baby Edmontosaurus all summer, but now has to chase smaller, more difficult prey as the baby Edmontosaurus are too large to hunt. He chases after an Alphadon, but another clawed foot grabs the fleeing mammal; that of another Troodon, and Patch is becoming impatient. The plentiful food for Scar is ending as well, as the dark, cold Arctic winter is approaching. When night falls for the first time, Scar has loses sign of the herd and spots a dark shape, which turns out to be a Gorgosaurus, which slices his face as he narrowly dodges the killer blow. Later, a herd of Pachyrhinosaurus arrives and starts to compete for the dwindling food supply, further pressuring the herd's search for food. Scar finds the Edmontonia feasting on insect larvae from a fallen tree branch and tries his luck with mixed success. The sun sets and the Pachyrhinosaur herd moves on somewhere else in search of food. The winter's approach causes the herbivores to start risking their safety and a young female Edmontosaurus gets killed by the Gorgosaurus as she wanders too far from the herd. The next day, the Edmontosaurus and Pachyrhinosaurus herds move south for the winter, while Edmontonia stays behind. She's way too heavy and her armoured body has been storing fat to last her through the lean months. Meanwhile, Patch and the Troodons are feasting on the dead female Edmontosaurus when the Gorgosaurus appears. The tyrannosaur scares the Troodons away, but is wounded in the fight, and Patch is frustrated and must work harder to find prey. Far away, the dinosaur herd is moving on, until Scar sees a dark shadows, which turns out to be a flock of scavenging Quetzalcoatlus, the biggest pterosaurs ever, which feed on the dying herd members that could not keep pace. The blizzard arrives and Scar collapses, but an older male arrives and helps him to keep moving through the blizzard. They continue on walking and don't realize they are heading into a trap; the ground breaks apart, meaning that they walked onto a frozen lake. As the herd struggles to escape the icy water, several get dragged under by mosasaurs known as Prognathodon. Scar has never swum before, but he is pushed in and starts to swim for the shore. In the Arctic, Patch picks up a bone and heads back to his nest, which he has been building in the hopes of attracting a mate. Nearby, The Gorgosaurus finds the Edmontonia outside its lair, but the bite to its leg is badly infected and it goes back into the cave to wait for easier prey to wander close. A thousand miles away, the Edmontosaurus herd moves on through a volcanic ash field. Lying in wait, a pack of Albertosaurus sleeps until the herd is close enough to ambush. The feathered carnivores wake up and start to stalk the herd. Scar runs for his life while one of the predators is hot on his heels. During the attack, an avalanche of water, rock and mud caused by the eruption that follows the attack slides down the bank. Scar climbs up the cliff, but loses his courage, and the Albertosaurus, injured in the eruption, begins to close in. Just as Scar sees the avalanche, he rushes up the cliff while the Albertosaurus is swept to its seeming death. Back in the Arctic, Patch tries to impress the female by dancing only to lose out to a more experienced male and the Edmontonia has found a last leaf. Suddenly, the log it stands on breaks apart and the Edmontonia slides down the snow on her back and crashes into a snowdrift, utterly helpless. Far away from the Troodons, Scar tries to call for his family, but the only calls are the ones that didn't make it; the old male Edmontosaurus he has been traveling with and an injured female Pachyrhinosaurus. The Albertosaurus, having survived the mudslide, rises back to its feet and starting following Scar's trail again. Scar and the old Edmontosaurus walks on, but the older animal, suffering from a brain tumor, becomes more aggressive and nervous towards Scar, eventually even biting him. Scar sees the Albertosaurus first, and flees. The old bull Edmontosaur fights the predator until they both tumble over the cliff, locked in a deadly embrace. In the frozen north, Patch learns how to finally catch Alphadon by listening for them under the snow and comes across the overturned Edmontonia. He and several other Troodons attack the ankylosaur, but the Gorgosaurus, now fully healed of its injury, arrives and pulls the herbivore away from the smaller predators. Struggling, the Edmontonia gets back up and injures the Gorgosaurus with her shoulder spikes. The Gorgosaurus heads back to the cave, fatally wounded with a broken leg. As the sun rises the next morning, Scar is becoming weaker and the Quetzalcoatlus that follows senses it. The young dinosaur hears a rustling noise, which turns to be the injured female Pachyrhinosaurus instead. The pterosaur gives up and the ceratopsian herd arrives to cross the river. As they cross the river, groups of Prognathodon arrive and pull many of them underwater. Scar dives in while the mosasaurs continue their attack on the Pachyrhinosauruses. Scar eventually reaches the far bank and reunites with the Edmontosaurus herd, finally reaching safety. The sun eventually rises again and warmth begins to spread across the Arctic Circle. The Edmontonia is feasting on the budding greens and Patch manages to find a mate, offering scavenged meat from the dead Gorgosaurus. Soon, the Edmontosaurus will travel north again once summer begins to arrive to the north.