Six years after the disaster on Jurassic Park, eccentric mathematician Ian Malcolm (whose death in the previous novel was retconned) and spoiled, rich genius Richard Levine are researching InGen's mysterious Site B, and its exact location, after learning of its existence. Site B, an island named Isla Sorna, was the secret "production factory" for Jurassic Park, where dinosaur stock were hatched and grown, before shipment to Isla Nublar. Levine mysteriously disappears, and Malcolm fears he might have discovered the location of Site B, and in his impatience already set out for it without letting Malcolm know. Custom field vehicle creator Doc Thorne and his employee Eddie Carr, who provided much of Levine's equipment, deduce the location of Site B, with the assistance of Malcom and two schoolchildren who assisted Levine, computer whiz R.B. "Arby" Benton and his friend Kelly Curtis. They organize a rescue operation and take with them two highly customized RVs, modified for scientific purposes, as well as a solar powered Ford Explorer, a motorcycle, and an observation platform called a 'high hide'. Stowed away with them as they leave are Arby and Kelly, who plan to rescue Levine as well.
At the same time, Lewis Dodgson, geneticist at Biosyn – InGen's arch rival – and two colleagues head to Isla Sorna, hoping to steal dinosaur eggs for their own company. Sarah Harding, a wildlife observer who had a previous relationship with Malcolm, accompanies them on the trip to the island. Dodgson throws Sarah overboard from their ship, thinking she will drown, and continues with his plan. Dodgson locates a nest of the Tyrannosaurus rex and, accompanied by George Basleton and Howard King, walks up to the eggs, carrying a box that emits painful ultrasonic frequencies that fend off the grown Tyrannosaurs. Dodgson tells Basleton and King to grab the eggs while he holds the adult dinosaurs at bay with the box, but Basleton freezes in fright once he sees the parents. Dodgson is forced to try to retrieve the eggs himself. While walking closer to the eggs, he steps on a hatchling Tyrannosaur, breaking its leg. The power cord for the box is pulled out of its battery pack, leaving the men defenseless. It takes the adult Tyrannosaurs a while to notice that the ultrasonic noise had stopped, but they soon move forward and attack Basleton, killing him. Dodgson makes a run for the SUV, but one Tyrannosaur pushes it off the hill before he can drive away. Dodgson falls out of the vehicle but survives. King is later killed by Velociraptors as he attempts to make his way across the island to the boat.
Coming across the baby Tyrannosaur, Eddie brings it back to the base camp, where Malcolm and Sarah fix its broken leg. The absence of the infant is noted by its parents, who track their offspring down by smell, leading them directly to the trailers. The T-Rex then pushes one of the trailers off the cliff, with Malcolm and Sarah inside. Both are rescued by Thorne, but Malcom's leg is injured, and he ends up spending most of the remainder of the story immobile and high on morphine (as he did in the previous novel). Meanwhile the group at the "high hide" are attacked by Velociraptors, who kill Eddie and abduct Arby. Thorne and Levine rescue Arby, and the survivors take shelter in an abandoned gas station set up by InGen for the island's workers when the island was still in use. There they encounter two Carnotaurus, but they manage to scare them away with flashlights.
Once daylight comes, Sarah attempts to get the Explorer back. After escaping a group of aggressive Pachycephalosaurus by hiding underneath the vehicle, she encounters Dodgson, who is also hunting for the SUV. Sarah pushes Dodgson out from under the vehicle, as revenge for his earlier attempt to murder her. He is then taken by one of Tyrannosaurs to their nesting site, where his leg is broken and he is left for the babies to eat. After Sarah fails to reach the helicopter in time, Kelly locates an abandoned building with a functional boat inside. After making a quick getaway from a group of Velociraptors, the survivors are able to reach the boat and escape the island. While on the boat, Malcolm and Harding tell Levine, to his dismay, that some of the carnivores, including the Velociraptors and the Procompsognathus, are infected with prions, and any animal bitten by them will be infected also. This means that all the dinosaurs on the island are fated to die due to spread of the prions. With that said, Thorne finally declares that is time for all of them to go home.
As with the first book, the characters have to fend off attacks from Tyrannosaurus and Velociraptor. Throughout the novel, Malcolm and Levine talk about various evolutionary and extinction theories, as well as the nature of modern science and the homogenizing and destructive nature of humanity. The book also discusses the role of prions in brain diseases, which has been at the root of concerns over Mad Cow Disease.
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