Plot
Crysta is a curious young fairy who lives in FernGully, a secluded rainforest east of Mount Warning. The fairies of FernGully once lived in harmony with humans, who are believed to be extinct after having been driven away by Hexxus, the dreaded spirit of destruction. Crysta is the apprentice of Magi Lune, the fairy tribe's leader, who ended Hexxus's reign by sealing him inside a boab tree. One day, Crysta explores a new part of the forest and meets Batty Koda, a cowardly but comical bat who was experimented on by humans, giving him a manic and deluded personality, and an electric device sticking out of his head. Crysta accompanies Batty to investigate the humans' potential return. She meets Zak, a young teenage logger whom she inadvertently shrinks when she tries saving him from being crushed by a falling tree, although she does not know how to restore him to normal size. After she rescues him from being eaten by Lou, a hungry goanna, Zak gains Crysta's trust and agrees to go with her to FernGully so Magi can unshrink him. Along the way, they bond by talking about their lives, but Zak hides the true reason for the humans' return.
Meanwhile, the tree containing Hexxus, which Zak accidentally marked while using his spray can against a fly, is cut down and processed by his supervisors, Tony and Ralph, using a mobile sawmill. Freed from his imprisonment, Hexxus quickly regains his powers by consuming the machine's polluting elements, and tricks Tony and Ralph into driving to FernGully. In FernGully, Crysta and Zak fall in love, but they soon discover the forest's destruction by Hexxus and the machine, exposing Zak's lie about the humans' intentions. Feeling betrayed, Crysta runs off as Zak comes clean. Magi sacrifices herself to give the fairies a chance to fight back, telling Crysta to remember what she has learned.
The next morning, Hexxus and the machine arrive in FernGully. Knowing the fairies' fight is hopeless, Zak convinces Batty to help him stop the machine before it destroys them. Hexxus seemingly kills Batty and scares Tony and Ralph away, but Zak, with Pips's help, manages to access the machine's cab and disable it, cutting Hexxus off from the emissions he drew upon. With Hexxus still manifesting via the oil in the machine, Crysta takes a seed and allows him to devour her, causing a tree to start growing from inside of him. Pips and the other fairies use the powers Magi bestowed them with to re-imprison Hexxus, along with the machine, within the new tree at FernGully's border. With FernGully saved, Crysta reunites with Zak and succeeds Magi as head of the fairy clan. She gives Zak a seed, asking him to remember his adventure and its lessons, before solemnly restoring him to his human size. Zak finds and revives Batty, reunites with Tony and Ralph, and plants the seed as Crysta looks on. With Hexxus defeated, the humans leave the forest and Crysta helps the seed sprout new growth for FernGully before playfully chasing Pips, with Batty following.