When a sprite named Crysta shrinks a human boy, Zak, down to her size, he vows to help the magical fairy folk stop a greedy logging company from destroying their home: the pristine rainforest known as FernGully. Zak and his new friends fight to defend FernGully from lumberjacks — and the vengeful spirit they accidentally unleash after chopping down a magic tree.

Pips wants to see more of the outside world. Batty arrives in a panic, announcing that two human poachers are right behind him. Poachers show up with their dogs and promptly capture the three baby animals. Pips and the Beetle Boys volunteer to follow the humans to town and rescue the babies, convincing Batty to be their guide.