Crysta (Samantha Mathis) is a fairy who lives in FernGully, a rainforest in Australia, and has never seen a human before. In fact, she is told they are extinct. But when a logging company comes near the rainforest, she sees that they do exist, and even accidentally shrinks one of them: a boy named Zak (Jonathan Ward). Now her size, Zak sees the damage that the company does and helps Crysta to stop not only them, but an evil entity named Hexxus (Tim Curry), who feeds off pollution.