The fairies live in a peaceful place in the forest called FernGully, which has been protected for many years by Magi Lune (Grace Zabriskie), a wise fairy with strong powers. Her granddaughter Crysta (Samantha Mathis) is a charming, beautiful fairy that is very intrigued about the world outside of FernGully. She, along with the other fairies in the forest, does not believe humans exist, and are only in stories, until a crazy bat by the name of Batty Koda (Robin Williams), comes and tells them all of these crazy stories about how he was captured by humans and experimented on. At first, no one believes him except Crysta, and she is determined to find out if humans are real. She goes to a place called Mount Warning, where the evil shadow of destruction, Hexxus (Tim Curry), is known to be trapped, and finds a human named Zak (Jonathan Ward). When he is almost crushed by a tree, Crysta accidentally shrinks him to fairy-size and he falls on a tree that is about to be devoured by "The Leveller". "The Leveller" is a wood-cutting machine that has been cutting down every tree the humans have been putting red Xs on. Crysta saves Zak from "The Leveller", which she thinks is just a monster, but she cannot properly un-shrink him. To avoid her being mad at him, Zak tells her that the red Xs keep the monster back, instead of for what they are really there, which is to pick which trees to cut down. They decide to take Zak to Magi Lune, so she can un-shrink him. On the way, Zak sees the forest really for the first time with all of its beauty and life. Back toward Mount Warning, the humans have accidentally released Hexxus, who is set on destroying FernGully, he uses "The Leveller" to cut down all of the trees to FernGully. When Crysta, Zak, and Batty Koda make it back to FernGully, the fairies cannot believe that Zak is really a human, and they're all excited to see him and learn about him. The only one who is truly worried is Magi Lune. She goes to check on the path to FernGully and sees that it is beginning to be destroyed and Hexxus is coming this way. She shows Crysta the red Xs and tells her the trees cannot be saved. With Hexxus drawing closer and closer to FernGully, Magi Lune calls for all of the fairies to come around to tells them of the danger. She uses the last of her magic to try and protect FernGully.