On InGen's second Costa Rican island, the dinosaur-manufacturing and cloning facility code-named Site B has been destroyed by a hurricane and the animals now live and breed in the wild. John Hammond (Richard Attenborough), having been removed from control of InGen, sees this as a chance to redeem himself by studying the dinosaurs in their natural state. He sends an expedition to reach the island before his nephew, Peter Ludlow (Arliss Howard), who intends to harvest the "significant productive assets" from the island.

Hammond's choice to lead the venture is Ian Malcolm (Jeff Goldblum), one of the survivors of the Jurassic Park debacle. Malcolm refuses to be involved until he learns that Dr. Sarah Harding (Julianne Moore), his girlfriend, is already on the island. It's a race between two philosophically opposed expeditions - one sent to protect the sanctity of the habitat and the other to round up the animals for commercial exploitation. But for Malcolm, the only one who appreciates the danger, it's a race to get out alive.