This story takes place six years after the Jurassic Park disaster.
The book starts out with Ian Malcom giving a speech on his theory of extinction at a place called the Santa Fe Institute. As he's talking, a tall man stands up. His name is Richard Levine. He's a paleontologist, and he is fairly wealthy. He interrupts Ian to tell him that he doesn't think dinosaurs are really extinct. He believes there's a lost world on an island somewhere off Costa Rica.
"I'm quite serious. What if the dinosaurs did not become extinct? What if they still exist? Somewhere in an isolated spot on the planet?" (5) Ian tells him this is nonsense, and continues on explaining his theory.
Outside of the Santa Fe Institute, Ian meets up with his long time friend, Sarah Harding, a well-known biologist who studies large predators in Africa. They discuss what Levine said, and they come to the mutual conclusion that Levine probably doesn't know what he's talking about.
Meanwhile, Levine is secretly preparing equipment for a jungle expedition. He enlists the help of a man called Doc Thorne, who was a college engineering professor, but now designs souped-up vehicles for expeditions and searches. He also enlists Doc Thorne's best mechanic, Eddie Carr. Levine has Doc Thorne and Eddie rig a Ford Explorer and a motorcycle to run on batteries. He also has them build reinforced trailers to house biological labs. Levine inspects the equipment and sees that it is satisfactory and almost ready to go. He suggests that instead of testing the prototype vehicles first, they take them directly to Costa Rica to start the expedition. Thorne doesn't like the idea, but because Levine is so enthusiastic, he agrees. Levine sets to leave at midnight from San Francisco, and the expedition is to join him in Costa Rica about forty-eight hours later.
As they're finalizing their plans for the trip, a black kid, Arby Benton, about ten years old, wearing glasses and a suit, and a taller white girl named Kelly Curtis walk in and catch wind of the plan and immediately want to go. They had been expecting to go on another small expedition with Levine over their spring break to study fossils having already had permission from their parents. Since they already had permission to be away from home, they decided it wouldn't hurt to go a little farther. Levine, Thorne and Eddie immediately say, "No," thinking that the risk would be too high. Levine leaves later that night for Costa Rica.
Back at the Santa Fe Institute, Malcom says goodbye to Sarah, because she is going back to Africa to continue her study of hyenas. As Malcom watches her leave, he decides to go visit his friend Doc Thorne in a day or two.
Levine reaches Costa Rica the next day and charters a fishing boat to bring him to Isla Sorna, one of five islands in a chain known as the "Five Deaths." Satellite evidence indicates to Levine that a volcanic island in this area may be home to nests of living dinosaurs. Before Levine leaves for the island, he hires a local guide, named Diego, who visited the island frequently as a child and claims to have knowledge of the island's trails and primitive roads.
They set out for Sorna and reach it two hours later. Levine and Diego are forced to climb steep cliffs to reach the plateau at the top of the island. As they reach the top, Diego looks around and confidently tells Levine to follow him. Diego leads the way to a stream where Levine stoops down to take a drink. In the undergrowth around him, he notices several small, chicken-sized dinosaurs. He recognizes them as procompsagnathuses. Diego also notices them and reaches out his hand to pet them. Levine warns him that even though these dinosaurs are small, it's possible that they could have a venomous bite. Diego quickly pulls his hand back just as one of the dinosaurs jumps at him and tries to bite him. Suddenly, the little dinosaurs begin to chirp and become skittish. They quickly scatter into the underbrush and disappear. Levine looks around worriedly for a some sign of what has frightened the diminutive dinosaurs. As he glances around, he can tell something is wrong, but he can't put his finger on what it is. Suddenly, Diego is jerked from his feet and dragged screaming into the surrounding bushes. Levine fills with panic and blindly begins running into the jungle. He doesn't make it far, however, before he is smashed from behind. He is saved only by his backpack, which the animal on top of him begins to tear to shreds. Levine manages to struggle loose from his back pack and quickly scrambles up the nearest tree.
Back in San Francisco, Malcom opens the door to Thorne's office and sees him sitting at a computer console with Arby and Kelly. Before Malcom can say "Hi," the satellite phone on Thorne's desk rings. He picks up the phone, only to hear static and the words, "Help...trapped...Isla Sorna." They recognize Levine's fear-stricken voice immediately. Then the connection goes dead. Thorne looks at Malcom and tells him to contact Sarah Harding and have her meet them on Isla Sorna as soon as possible.
Then Thorne sends Arby and Kelly home, after steadfastly denying their request to go on the expedition, stating that it would be too dangerous. Arby and Kelly act as if they are leaving, but sneak into a trailer as stowaways in a cabinet.
Meanwhile, at a cafe in Chinatown, Lewis Dodgson, a researcher for the Biosyn Corporation, learns from his spies of Richard Levine's expedition to Isla Sorna. He decides to take advantage of the situation and take his own expedition to Isla Sorna. He intends to steal Levine's research and pass it off as his own. He also plans to collect an egg from each species of dinosaur. He and his accomplice, Howard King, another researcher at Biosyn, and the unwitting Professor George Basilton decide to head to Costa Rica and get to Isla Sorna as quickly as possible.
In Africa, Sarah gets Ian's phone call while she is studying a hyena kill of an African bison on the savannah. She's learns of Richard's dire predicament and says that she will meet the expedition on Isla Sorna as soon as she can.
Doc Thorne, Ian Malcom and Eddie Carr reach Puerto Cortez in Costa Rica the next day and waste no time in getting their equipment ready for sling loading by helicopter to Isla Sorna.
They reach the Island an hour later and land in a grassy clearing in the jungle. The helicopters leave, and the members of the expedition set about readying their equipment. Eddie drives the battery-powered Explorer out into the open and is followed by Ian and Thorne, who are driving the lab trailer. Eddie leads the way down what appears to be an old, overgrown jungle road. After about a half mile, Eddy stops at a stream. He flips on a radar monitor to see if he can detect the sensor that was carried by Levine. A red dot, indicating Levine's position, flashes on the monitor. Eddy conveys to the rest of the team that he has a visual on Levine's position. They decide to press on.
After another half mile, they come to a fork in the road. A nearby sign points left to "swamp." To the right it points to "Site B." They mutually agree to investigate Site B. Eddy puts his foot on the gas, but abruptly stops. Over the CB, his shocked voice can be heard saying, "What's that!?" They all gaze in the direction he's pointing, just in time to see a dinosaur the size of a cow cross the road, followed closely by a dinosaur three times that size with a bony frill on its neck and three large horns. Ian calmly explains, "That's a triceratops. A young one, by the looks of it." (125) Everyone watches in amazement as the dinosaurs trundle across the road and disappear into the trees.