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 group of Compsognathus.
John Hammond invites mathematician Dr. Ian Malcolm to discuss the recent incident. InGen is now headed by Hammond’s nephew Peter Ludlow, who used the incident to gain control of the company from Hammond. Ian learns that InGen had originally created the Jurassic Park dinosaurs on Isla Sorna but the island was abandoned during a storm and that the animals were released into the wild to fend for themselves. Ludlow now wants to exploit the island’s creatures to save InGen from bankruptcy. Hammond asks Ian to join a team who will document the dinosaurs in their natural habitat, in order to encourage a policy of non-interference. Ian’s girlfriend, paleontologist Dr. Sarah Harding, was hired and is already on Isla Sorna. Upon learning this, Ian reluctantly agrees to go to the island, but only to retrieve Sarah.
Ian travels to Isla Sorna with Eddie Carr, an equipment specialist and engineer, and Nick Van Owen, a video documentarian and activist. Ian is shocked to find his daughter Kelly stowed away with them in a trailer, which serves as their mobile base on the island. They also find Sarah, but she is insistent on staying to continue her research. The group discovers that Ludlow is also on the island and capturing large numbers of dinosaurs with help from teams of mercenaries, hunters and palaeontologists including big game hunters Roland Tembo and Ajay Sidhu; Roland’s second-in-command, Dieter Stark; and paleontologist Dr. Robert Burke.
Malcolm’s group learns that Ludlow and the InGen team are planning to ship the captured specimens to a proposed Jurassic Park attraction in San Diego. Nick and Sarah free the captured dinosaurs, who wreak havoc across the InGen team’s camp. On the way back to the mobile 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 the Tyrannosaurus adults arrive. They reclaim their infant, destroy the trailer, and devour Eddie.
Ian and his group are rescued by Ludlow’s team, and both are forced to work together after losing all their communications equipment. They decide to reach an abandoned InGen site to call for help. Dieter is later separated from everyone else while trying to relieve himself in the wilderness, where he is killed by a group of Compsognathus. After the team sets up a camp for the night, they are ambushed by the Tyrannosaurus adults: Burke is devoured, and everyone else flees into a field of long grass containing a pack of Velociraptors, which kill Ajay and others.
Ian, 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.
Later, Ian and Sarah attempt to meet with Ludlow in San Diego to convince him to abandon his plans, only for the ship carrying the male Tyrannosaurus to suddenly crash into the docks. The crew is found to have been killed, and the male is accidentally released and goes on a rampage in the city. Ian and Sarah learn that the infant was taken directly to the planned theme park, so they retrieve it and use it as bait to lure the male back to the docks: Ludlow is cornered by both dinosaurs in the cargo hold of the ship, crippled by the adult and mauled to death by the infant. Sarah uses a tranquilizer gun to sedate the male, while Ian seals the cargo hold doors and police arrive to secure the scene.
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.