Crysta, a curious fairy apprentice to Magi Lune, shrinks logger Zak and enlists him to help stop a mobile sawmill called the Leveler from destroying FernGully, while battling the pollution-fueled spirit Hexxus released from a felled tree. The story emphasizes environmental harmony, friendship between Crysta and Zak, and personal redemption as Zak turns against the logging operation, but frames these through traditional fairy-tale tropes and a supernatural villain rather than modern activist framing.

This approach aligns with 1990s mainstream eco-messages without injecting identity politics or critiques of traditional norms. All characters are original creations with no race, gender, or sexuality alterations to established figures, as seen in the voice cast featuring Samantha Mathis as Crysta and Jonathan Ward as Zak. Creator statements highlight an intent to deliver an entertaining environmental message without preaching, resulting in a low woke score. The film avoids DEI mandates or foregrounding of contemporary social issues, keeping the focus on straightforward storytelling and the personified threat of pollution embodied by Hexxus.