Muldoon and Gennaro go out to investigate the hadrosaur stampede. Arnold informs them that he has found Nedry. Once they reach him, they retrieve the rocket launcher and leave Nedry's carcass to the compys, which Gennaro notices have five-fingered hands. Grant and the kids float under the giant dome of the park's aviary.
Arnold monitors the motion sensors but is unable to locate either the t-rex or Grant and the kids. Malcolm claims that a part of his theory, the "Malcolm Effect," indicates that a catastrophic event will happen when it appears the system is working perfectly.
Inside the aviary, Grant and the kids are looking for motion detectors and are attacked by fiercely territorial cearadactyls, large fish-eating pterodactyls. One of them tries to pick up Lex, but Grant fights it off. They escape back to the raft. Unsure what to do when they are confronted by a group of poisonous dilophosaurs by the shore, Grant and company are saved when the t-rex reappears and distracts the dilophosaurs long enough to allow the raft to pass.
Arnold finally locates the t-rex, and Muldoon and Gennaro go to catch it. Muldoon fires two rocket-launched doses of tranquilizer at the tyrannosaur but seems to miss, and they are forced to flee. The t-rex turns around and again chases Grant and the kids, who fall down a waterfall. Lex narrowly escapes the tyrannosaur, nearly drowning in the process. They run behind the waterfall to escape, and Grant finds a maintenance door and enters it, only to be trapped inside. He finds a flashlight, a baby male velociraptor, and an electric go- cart. Outside, the t-rex finds the kids behind the waterfall and starts dragging Tim out with its tongue. Suddenly, the dinosaur keels over.
Arnold reports that the t-rex finally succumbed to its tranquilizer dose, as Muldoon had not missed after all. Just as Arnold is gloating that things are back in order, he notices that the park has been running on its auxiliary power, and that the power has suddenly run out. He realizes there was a mix-up when he shut the power off earlier. Meanwhile, the waterfall stops flowing and the maintenance door opens, releasing Grant.
Back at the control room, Wu reads a printout that indicates that the electric fences have been off for the last five hours. Arnold goes out to try to turn the generator back on, but is killed by a velociraptor. Muldoon and Gennaro narrowly escape the pack of raptors, but Gennaro is attacked by a raptor when he goes back to the generator to try to turn it on again.
Grant and the kids take the go-cart back to the visitor center, which is in shambles. Wu, Harding, Muldoon, Sattler, Hammond, and Malcolm are all trapped in a room at the lodge, as three raptors on the roof of the room slowly bite through the bars of the skylight. Sattler goes outside to distract the raptors while Grant makes a run for the generator, leaving the kids alone in the cafeteria.
Sattler draws the attention of two more raptors, but it turns out that these two are merely distracting her while the raptors on the roof come to attack her from behind. Wu steps outside to warn Sattler what is happening. He is killed by a raptor that jumps from the roof, but Sattler escapes. Grant discovers Gennaro still alive and turns on the generator. A raptor sneaks into the cafeteria but Tim locks it in the freezer. He and Lex flee to the control room and find a radio. Muldoon tells Tim that he must turn on the electricity since none of the people who are still alive knows how to use computers.
Tim fiddles with the computer controls, but he and Lex are forced to leave the room when three raptors appear on the balcony. In the hallway, the kids realize that Tim had somehow turned on the electronic door locks, locking them out of every room. They find a security card on a dead guard and use it to open the nearest door.
The raptors follow the kids into the nursery. Tim throws the baby raptor at the attacking adults, who tear it to shreds. The kids run into the next room, meeting up with Grant and Gennaro. Grant distracts the raptors while Gennaro takes the kids and runs into the next room, but they are trapped there. Grant lures the raptors into the laboratory, where he kills two of them by feeding them dinosaur eggs that he has injected with poison. He injects the poison directly into the tail of the third raptor with a syringe. After it dies, he and the others run to the control room.
Tim manages to turn the electricity on just in time, and the bars on the skylight now keep the raptors out. The group calls the supply ship that has the stowaway raptors aboard, instructing it to turn around just before it docks into Costa Rica.
Hammond sighs, relieved that his dinosaurs have not gotten free to overrun the world. Malcolm calls Hammond an egomaniacal idiot for thinking that he could ever be directly responsible for destroying the entire planet. Man will never be able to destroy the planet, he contends.
A helicopter and the Costa Rican National Guard are on the way. Grant, Sattler, Muldoon, and a reluctant Gennaro go to find the raptor nest to determine if any animals have gotten off the island. On the way, Grant explains how the dinosaurs were able to reproduce: certain species of frogs can spontaneously change their gender when they are in an environment in which all of the animals are the same sex. The dinosaurs with the frog DNA, therefore, must have retained that trait. Once they are at the raptor nest, Gennaro refuses to go down the nest hole, but Grant says he must own up to his responsibility.
Hammond takes a walk and muses that, even if Gennaro shuts down his island, he still has frozen embryos safely stored in California. Tim and Lex fool around in the control room, playing a recorded tyrannosaur roar over the park's loudspeakers. Hammond hears the roar and, thinking he is about to be attacked, trips and falls down a ravine.
Grant and Sattler go down the hole of the raptor nest and Muldoon forces Gennaro to follow. The large manmade cavern is teeming with raptors of all ages. The three observe the animals as they seem to line up and suddenly all run down a concrete tunnel.
Hammond is attacked and overwhelmed by a group of compys.
Grant, Sattler, and Gennaro follow the raptors, emerging from the tunnel on the beach. The raptors again line up in a northeast-southwest formation and Grant assumes that they want to migrate.
Helicopters scare off the raptors while soldiers take Grant, Sattler, and Gennaro into a chopper where Muldoon and the kids are already on board. Muldoon informs them that Hammond and Malcolm are dead. The soldiers want to know who is in charge, but no one is.
The government retains everyone at a hotel for questioning. Guitierrez comes to visit and informs Grant that some animals had been eating local crops in a peculiar manner. They moved in a straight line from the coast into the mountain jungle, eating agama beans and soy—foods rich in lysine. The animals disappeared into the jungle, and now no one knows where they are.
As the novel closes, we see that many characters meet fates that can been seen as appropriate or just deserts. Nedry, who endangers the entire island through his greed, is killed by dilophosaurs. Muldoon even notes the appropriateness of his demise after he finds Nedry's carcass: "Maybe there's justice in the world after all." Regis cowardly abandons the children, and in so doing seals his own fate. Although Hammond claims to have created the park for the children of the world, he modifies this statement and admits that only the world's richest kids would ever get to see his dinosaurs. Ultimately, all Hammond wants is to make a lot of money. Even after witnessing all the death and destruction his scheme causes on Isla Nublar, Hammond still intends to make another park with frozen embryos that he has in storage. The fact that his death comes about due to his own grandchildren, albeit accidentally and indirectly, adds irony to his fate.
Similarly, Arnold, so certain that he has everything under control, allows his confidence to lead to carelessness. It is fitting that he dies while trying to cover for his mistake, that he left the auxiliary power on. Dr. Wu never intends any harm, but conducts his manipulation of biology and genetics with such ignorance for the animals he is creating that it is no wonder he pays a price for messing with nature. Likewise, Gennaro, though always skeptical that Jurassic Park is not safe enough for visitors, still schemes about making a fortune from Hammond's idea. Though Gennaro manages to survive, Grant forces him to help scope out the raptor nest before he leaves the island— a duty that Gennaro initially refuses to accept. Grant is adamant, however, that take responsibility for his part in creating this park. In a sense, then, though Gennaro survives, he nonetheless pays his dues.
Meanwhile, the main protagonists and seemingly responsible characters—Grant, Sattler, Tim, and Lex—all survive virtually unscratched. Muldoon, who always has had reservations about the park's safety and Hammond's methods, and who tirelessly fights to keep the dinosaurs in check, also makes it out alive. Harding, the unassuming vet whom we never see committing any significant wrong, manages to survive as well.
The only confusing character is Malcolm, who has all along told Hammond not to build the park because it is a bad idea. It may seem somewhat odd, then, that he dies. Perhaps Malcolm's certainty that chaos theory and its fatal implications for the island will prove true actually wills his own death in a sense. Alternatively, it may be that Crichton is merely rewarding Malcolm's smug, swaggering arrogance with particularly harsh retribution.