The game opens with John Hammond reading an excerpt from his memoirs. Hammond is a rich industrialist who used his wealth to assemble a scientific team that cloned dinosaurs. Intent on creating an amusement park showcasing his biological attractions, Hammond's park ultimately fails when the dinosaurs escape. While Jurassic Park was built on Isla Nublar, off the coast of Costa Rica, the animals were raised at an alternate location, Isla Sorna, also named "Site B". Trespasser takes place a year after the events of The Lost World: Jurassic Park, where the general public has learned about the existence of Jurassic Park.
The game begins in a dark apartment, where mail is piling up and a phone rings. When it goes to voice-mail, a woman named Jill leaves a message, expressing amazement that Anne (the apartment's resident) had actually gone ahead on a trip to the tropics. The message closes with Jill's comment, "I thought you HATED flying." The scene changes to an unseen person closing and bolting an airplane bathroom door and then the sounds of retching can be heard. The plane suddenly bucks and an apparent malfunction occurs and the plane crashes.
Anne awakens on the shores of an island (apparently the sole survivor of the crash), and proceeds to explore. Anne learns she is on Site B, InGen's dinosaur breeding facility. Pursued by dinosaurs, Anne makes use of weapons left behind to defend herself as she explores. Following a monorail track into the island interior, Anne encounters dinosaurs such as Brachiosaurus, Velociraptor, Stegosaurus, Triceratops, Tyrannosaurus, Parasaurolophus, and Albertosaurus. After recovering security cards from an InGen town, Anne proceeds past a dam and to a large mountain. At the summit, Anne is able to contact the United States Navy on an emergency channel. After defeating the Alpha Velociraptor and its tribe that lives atop the mountain, she is rescued by helicopter. The game closes as Anne returns to her apartment. Jill calls and the message goes to the answering machine, saying she "better have a good damn reason for not calling," Anne wordlessly responds by tossing a raptor claw on her desk.
