The story follows Drake Gemini, his twin brother Jacob, and their father, who have been stranded on Dinotopia for 10 years.

At the beginning of the game, their father is attacked and killed by a rogue Tyrannosaurus while exploring the outer jungles of Dinotopia.

After this, Drake and Jacob go their separate ways. Jacob joins a gang of dinosaur-hating humans called the Outsiders, while Drake takes on the role of a guardian of Dinotopia.