Four years after the events on Isla Nublar, a wealthy family docks their yacht ashore at the nearby Isla Sorna. Their daughter wanders off to a nearby jungle, where she is attacked by a pack of Compsognathus, but survives.
John Hammond invites mathematician Dr. Ian Malcolm to discuss the recent incident. Malcolm learns that InGen, now headed by Hammond's nephew Peter Ludlow, created the dinosaurs for Jurassic Park on Isla Sorna. To prevent Ludlow from exploiting the creatures to save InGen from bankruptcy, Hammond asks Malcolm to lead a team who will document the dinosaurs in their natural habitat, in order to encourage a policy of non-interference. Malcolm reluctantly agrees when he learns that his girlfriend, paleontologist Dr. Sarah Harding, was hired and is already on the island.
Malcolm travels to Isla Sorna with Eddie Carr, an equipment specialist and engineer, and Nick Van Owen, a video documentarian and activist. Malcolm is shocked to find his daughter Kelly stowed away with them in a trailer, which serves as their mobile base on the island. Shortly after finding Sarah, the group discovers that Ludlow is also on the island and capturing large numbers of dinosaurs with help from a team of mercenaries including big game hunters Roland Tembo and Ajay Sidhu; Roland's second-in-command, Dieter Stark; and paleontologist Dr. Robert Burke.
Overseeing their camp at night, Malcolm's group finds out that Ludlow and the InGen team are planning to ship the captured specimens to a theme park in San Diego. Nick and Sarah free the captured dinosaurs, who immediately wreak havoc across the camp. On the way back to their base, Nick rescues an injured Tyrannosaurus rex infant that Roland hoped to use as bait to hunt its male parent. Nick and Sarah treat the infant for a broken leg, but despite their good intentions, the Tyrannosaurus adults arrive and reclaim their infant before destroying the base and killing Eddie.
After the dinosaurs leave, the group find themselves rescued by Ludlow's team, both of whom are forced to work together after losing all their equipment. With the Tyrannosaurus adults pursuing them, they decide to reach an abandoned InGen site to call for help. Dieter is later separated from everyone else and fatally attacked by a pack of Compsognathus. After the humans set up camp for the night, they are ambushed by the Tyrannosaurus adults: Burke is eaten, and everyone else flees into a field of long grass containing a pack of Velociraptors, which kill Ajay and many others.
Malcolm, Sarah, Kelly, and Nick manage to reach the InGen base, ward off more Velociraptors, and successfully radio for helicopter extraction. After being rescued, Nick reveals that he stole Roland's ammunition to prevent him killing his intended trophy, but they learn that Roland subdued the male Tyrannosaurus with tranquilizers instead. While more InGen personnel arrive on the island to secure the male and the infant for transportation, Roland declines a job offer at the San Diego park from Ludlow, reflecting on Ajay's death and questioning the morality of Ludlow's scheme. In the aftermath, with both dinosaurs on their way back to Isla Sorna, Hammond appears in a televised news interview to announce that the American and Costa Rican governments have declared the island a nature preserve, finishing the interview with same words Malcolm once said to him before - "life will find a way".
