The narrative begins by slowly tying together a series of incidents involving strange animal attacks in Costa Rica and on Isla Nublar, the main setting for the story. One of the species, a strange small lizard-like creature with three toes is identified later as a Procompsognathus. Paleontologist Alan Grant and his paleobotanist graduate student Ellie Sattler are abruptly whisked away by billionaire John Hammond (founder and chief executive officer of International Genetic Technologies, or InGen) for a weekend visit to a "biological preserve" he has established on an island 120 miles west off the coast of Costa Rica.
Recent events have spooked Hammond's considerable investors, so, to placate them, he means for Grant and Sattler to act as fresh consultants. They stand in counterbalance to a well-known mathematician and chaos theorist, Ian Malcolm, and a lawyer representing the investors, Donald Gennaro. Both are pessimistic, but Malcolm, having been consulted before the park's creation, is emphatic in his prediction that the park will collapse, as it is an unsustainable simple structure bluntly forced upon a complex system.
Upon arrival the park is revealed to contain cloned dinosaurs, which have been recreated using damaged DNA found in mosquitoes that sucked Saurian blood and were then trapped and preserved in amber. Gaps in the genetic code have been filled in with reptilian, avian, or amphibian DNA. To control the population, all specimens on the island are bred to be female as well as lysine-deficient. Hammond proudly showcases InGen's advances in genetic engineering and shows his guests through the island's vast array of automated systems.
Countering Malcolm's dire predictions with youthful energy, Hammond groups the consultants with his grandchildren, Tim and Alexis "Lex" Murphy. While touring the park with the children, Grant finds a Velociraptor eggshell, which seems to prove Malcolm's earlier assertion that the dinosaurs have been breeding against the geneticists' design (the population graphs proudly introduced earlier were naturally distributed, reflecting a breeding population, rather than displaying the distinct pattern that a population reared in batches ought to display).
Malcolm suggests a flaw in their method of analyzing dinosaur populations, in that motion detectors were set to search only for the expected number of creatures in the park and not for any higher number. The park's controllers are reluctant to admit that the park has long been operating beyond their constraints. Malcolm also points out the height distribution of the Procompsognathus forms a Gaussian distribution, the curve of a breeding population.
In the midst of this, the chief programmer of Jurassic Park's controlling software, Dennis Nedry, attempts corporate espionage for Lewis Dodgson, a geneticist and agent of InGen's archrival, Biosyn. By activating a backdoor he wrote into the system, Nedry manages to shut down the park's security systems and quickly steal 30 frozen embryos, two of each of the park's fifteen species. He then attempts to smuggle them out to a contact waiting at the auxiliary dock deep in the park. But his plan goes awry: during a sudden tropical storm Nedry becomes lost and stops his stolen Jeep at a dead end. He exits the Jeep to determine his location. A dilophosaurus approaches him from afar, blinds him with its poisonous saliva, and then kills him. Nedry's plan called for him to secretly deliver the embryos and return to the park's control room within fifteen minutes, but without him to quietly patch the system, the park's security is left off, leaving the electrified fences deactivated. Without the barriers to contain them, dinosaurs begin to escape. The adult and juvenile Tyrannosaurus rex attack the guests on tour, destroying the vehicles, killing InGen public relations manager Ed Regis, and leaving Grant and the children lost in the park. Ian Malcolm is gravely injured during the incident but is soon found by Gennaro and park game warden Robert Muldoon and spends the remainder of the novel slowly dying as, in between lucid lectures and morphine-induced rants, he tries to help those in the main compound understand their predicament and survive.
The park's upper management — engineer and park supervisor John Arnold, chief geneticist Henry Wu, Muldoon, and Hammond — struggle to return power to the park, while the veterinarian, Dr. Harding, takes care of the injured Malcolm. For a time they manage to get the park largely back in order, restoring the computer system by shutting down and restarting the power, resetting the system. Unfortunately, a series of errors on their part soon plunge the park into greater disarray. During their time trying to restore the park to working order, they fail to notice that the system has been running on auxiliary power since the restart, which soon runs out, shutting the park down a second time. The viciously intelligent Velociraptors, referred to by characters as "raptors", finally escape. They soon kill Wu and Arnold, and injure Muldoon, Gennaro, and Harding. Finally, Grant and the children slowly make their way back to the central compound, carrying news that several young raptors, bred and raised in the island's wilds, were on board the Anne B, the island's supply ship, when it departed for the mainland.
Grant is able to turn the main power back on, while Ellie distracts the raptors so that they won't get to him. After escaping from several raptors, Grant, Gennaro, Tim, and Lex are able to make it to the control room, where Tim is able to contact the Anne B and tell them to return. The survivors are then able to organize themselves and eventually secure their own lives. Word soon reaches them that the crew of the Anne B has discovered and killed the raptor stowaways.
Gennaro tries to order the island destroyed as a dangerous asset, but Grant rejects his authority, claiming that even though they cannot control the island, they have a responsibility to understand just what happened and how many dinosaurs have already escaped to the mainland. Finally Grant, Ellie, Muldoon, and Gennaro set out into the park to find the wild raptor nests and compare hatched eggs with the island's revised population tally. Cautious in this pursuit, they emerge unharmed. Meanwhile, Hammond, while taking a walk around the park, decides to salvage and restore the park to its original state, but gets injured, then killed and eaten by a pack of compys. Concerning the dinosaurs' breeding, it is eventually revealed that the frog DNA used to fill gaps in certain strands enabled some of the dinosaurs to change sex, as some species of frogs can do.
In the end the island is suddenly and violently demolished by the fictional Costa Rican Air Force (in reality, Costa Rica has no air force, nor any armed forces). It is stated that Malcolm dies and his burial is not permitted (although he is retconned to have survived in the sequel The Lost World). Survivors of the incident are indefinitely detained by the United States and Costa Rican governments. Weeks later, Grant is visited by Dr. Martin Guitierrez, an American doctor, who lives in Costa Rica and has found a Procompsognathus corpse. Guitierrez informs Grant that an unknown pack of animals has been eating crops rich in lysine (the molecule in which the animals were designed to be deficient) and killing chickens as they migrate toward the Costa Rican jungle. He also informs Grant that none of them, with the possible exception of Tim and Lex, are going to be leaving any time soon.
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