Four years after the incident at Jurassic Park, John Hammond (Richard Attenborough) has lost control of InGen to his nephew, Peter Ludlow (Arliss Howard). Ian Malcolm (Jeff Goldblum) violated his non-disclosure agreement and went public about the events, but few believed him and threats of legal action prevented him from producing any evidence, leaving his academic reputation destroyed. One day, Hammond summons Malcolm to his home and tells him about "Site B", located on Isla Sorna, where the dinosaurs were actually engineered, before being sent to Isla Nublar when mature. The island was abandoned after a hurricane wiped out most of the facilities, and the creatures were left there to live wild. Hammond asks Malcolm to help him stop Ludlow from using Site B to bail out the bankrupt InGen, and to help him convince environmentalists to leave the island as a nature reserve. Malcolm initially refuses, but agrees to go after learning that his girlfriend, paleontologist Sarah Harding (Julianne Moore), is already there.
Malcolm is joined by Eddie Carr (Richard Schiff), an engineer who built the group's custom vehicles, and Nick Van Owen (Vince Vaughn), documentary producer and environmentalist. Shortly after arriving on the island, they encounter a Stegosaurus herd and meet Sarah. When they return to camp, they find Kelly (Vanessa Lee Chester), Malcolm's daughter, has stowed away. Malcom tries to contact the boat to take them home, but they are interrupted by the arrival of an InGen team sent by Ludlow. The rival team quickly captures samples of several species, including Parasaurolophus, Stegosaurus, Gallimimus, Pachycephalosaurus, Triceratops, and a swarm of Compsognathus. That night, Nick and Sarah sneak into the InGen camp to free the dinosaurs and cut the fuel lines on the vehicles. The freed dinosaurs cause a huge commotion, compounded by the exploding vehicles. Roland (Pete Postlethwaite), the leader of the InGen team, admonishes his second-in-command, Dieter Stark (Peter Stormare), for the lack of security.
Roland wishes to kill an adult male Tyrannosaurus, and creates a trap by breaking the leg of a baby T. Rex so that its cries might lure its parents. When he returns to the camp, Nick frees the baby, taking it back to their trailer so Sarah can set its broken leg. The adult Tyrannosaurs come searching for their child and, after retrieving it, throws one half of the hinged trailer over a cliff with Malcolm, Nick, and Sarah inside. Eddie throws down a rope and tries to pull the trailer back up using one of the SUVs, but is torn in half and eaten by the Tyrannosaurs. The trailer falls off the cliff, but its occupants survive by holding on to the rope, only to be rescued by the InGen team. With all of the communications equipment destroyed in the attacks, both groups team up to reach the old InGen compound's radio station, right through a Velociraptor nesting site.
At night, the male Tyrannosaur comes across the group's camp and pokes his head into Sarah and Kelly's tent, sniffing Sarah's jacket covered with blood from the baby's leg. One of the InGen team workers notices this and screams, waking up the rest of the group as they all begin to run, with the female Tyrannosaur in pursuit. After initially failing to kill the male Tyrannosaur (mainly because Nick stole the bullets from his gun), Roland uses a tranquilizing gun to knock the dinosaur out. After fleeing the female Tyrannosaur, the InGen team passes through a field of tall grass and are picked off one-by-one by Velociraptors. Malcolm, Sarah, Nick, and Kelly pass through the field unharmed and Nick reaches the compound, but the others are attacked by three raptors and go into hiding. After a fight with the raptors, Ian, Sarah, and Kelly run towards a building where they reunite with Nick and contact a rescue helicopter. As they fly away, they see that Roland has caged the male Tyrannosaur and Ludlow preparing to ship it and the baby back to the mainland.
When the ship carrying the dinosaur arrives in San Diego, it crashes into the dock. A boarding party finds out the entire crew is dead. While searching for survivors, a guard opens the cargo hold and inadvertently releases the Tyrannosaur, which escapes into the city. Malcolm and Sarah learn that the Tyrannosaur stopped breathing due to a tranquilizer overdose, it was given amphetamines to bring it around, but not knowing the proper dosage, they administered too much and the dinosaur is out of control. Realizing that the Tyrannosaur will likely come for its infant, Malcolm and Sarah rush to the Jurassic Park arena to get the baby T. Rex, which had been brought in separately by plane, and during this time, the T. Rex is wreaking havoc in San Diego, having eaten a fleeing civilian and a dog. They lure the adult with the baby and run back to the boat. Ludlow tries to intervene, but is trapped in the cargo hold and devoured by the baby. Malcolm and Sarah manage to tranquilize the adult before it can escape again, and seal it in the hold.
By morning, as Malcolm and Sarah fall asleep on the couch in their living room, Kelly watches television reports of the cargo ship on its way back to Site B, surrounded by a convoy of naval vessels. The program breaks away to an interview of restored InGen Chairman John Hammond, who explains that the island will now be left alone as a natural reserve so the dinosaurs can live free of human interference. He offers a quote by Malcolm, "Life will find a way." The scene cuts to Site B, where the family of Tyrannosaurs is shown reunited in the wild, alongside a herd of Stegosaurus migrating and a flock of Pteranodons flying overhead.