Edge is a curious young scientist. She and her mother study the Insects, a race of creatures who communicate through dance and chemical signals. Edge believes she and her mother are the only animals on Crescent Island who can talk until she meets an outcast named Jessop and his friend Xalma, a mysterious child who lives in an underground lake called The Grotto. Edge’s new friends teach her things about the world that her mother has kept secret.

Xalma soon grows jealous of Jessop and Edge's new friendship, and she starts to treat Edge badly. After learning that Xalma has lived in The Grotto for over 600 years, Edge is abducted by a rover sent by Tsoci (The Spirit of Crescent Island), a superorganism that hosts all life on the island. Tsoci discovers that Edge has a power that no animal has ever had. She can 'merge' to experience the world from Tsoci's perspective, and survive.

The rover who abducts Edge gradually becomes a self-aware individual and begins to question Tsoci’s motives. After undergoing a physical transformation, the rover renames themself Sole, and offers to help Edge and her mother learn more about the Insects. After a disastrous encounter with the Insects, Edge's mother's memories are erased and her home is destroyed.

Tsoci agrees to order the Insects to return Mana's memories, but only if Edge embarks on a mission to discover the reason for her power to merge. In the meantime, Xalma's home is also destroyed, forcing her out of the place that has kept her from aging, and into the grasp of a rebel group called The Resistance. She is separated from Jessop, and undergoes a rapid and painful transition into adulthood.

Accompanied by Jessop and Sole, Edge leaves her sheltered valley and travels to a hidden forest city where The Resistance is preparing to wage war against Tsoci. Sole discovers that The Resistance has been experimenting on the Insects. Edge, Sole, and Jessop plan to rescue the Insects with help from a new Insect friend named Mary and a young Avian named Mahali.

Jessop and Xalma are reunited, but Xalma's self doubt and jealousy result in her departure from the group hours before the rescue takes place. She is convinced that Jessop’s new friends are going to harm him.

Xalma confronts Edge after the Insects have been rescued. Edge uses her power to merge to connect the minds of the Insects, Xalma, and members of The Resistance, changing their perspective and causing the members of The Resistance to switch sides and join Tsoci.

The leaders of The Resistance escape being connected through Edge’s power, and disclose that this power is not a surprise to them - they are responsible for engineering it as another weapon to use against Tsoci. They realize that Edge is acting on Tsoci's behalf, and try to destroy her along with anyone she has merged with.

Sole saves Edge, Jessop, Mary, and Mahali, but is unable to save most of the newly liberated Insects or the members of The Resistance. During the battle, Tsoci succeeds in infecting the leaders of The Resistance with a mysterious spore.

Edge wakes many days after the conflict. She does not remember the violence, and returns home to find her mother's memories returned. Her friends agree not to tell her about the violence until she has had a chance to experience peace for a while, and she recovers in safety, while Sole transports the survivors back to the valley and helps Edge's mother build a new home.