FernGully is a rain forest that is home to a race of fairies who have never seen humans and believe that they only exists in stories. That is, until the arrival of Batty, a wacky bat who tells the fairies that he has seen the humans. Curious when she sees smoke from Mount Warning, a fairy named Crysta travels beyond FernGully and discovers a group of humans is destroying the rain forest. Crysta discovers a human named Zak who is helping destroy the rain forest and accidentally shrinks him. After discovering the beauty of FernGully, Zak and Crysta learn that the fairies and FernGully itself are in mortal danger. The humans have freed Hexxus, an evil oil-like creature who a long time ago was turned into a tree when he tried to unleash chaos in FernGully. Hexxus has taken over "The Leveler" a logging machine, and he begins his evil scheme to destroy FernGully. Only Zak, Crysta, Batty, Pips and the Beetle Boys can defeat Hexxus and save FernGully from destruction.