
When Rubes transforms into a Flame Squirrel on his eighth birthday, he must learn to embrace his analytical approach to fire abilities while helping Pip rescue a mysterious butterfly squirrel created in Thornok's laboratory. Together with their family and friends, they embark on a dangerous journey through Whistle Woods to save Baby Pip and help her find freedom.
Rubes anxiously awaits his type revelation on his sixth birthday, hoping to become a rare Legendary or Mythical type. When he transforms into a Flame Squirrel instead, he feels disappointed despite his family's support. Mechanical spy drones observe the ceremony from afar, while Thornok begins an experiment with Baby Pip.
Rubes struggles in traditional Flame Squirrel training, finding the emotional approach doesn't work for him. With help from Evie the Quantum Abacus Squirrel, he discovers his analytical approach to fire could be groundbreaking. Meanwhile, Thornok monitors his development with interest.
Pip and Rubes discover one of Thornok's damaged spy drones in the forest. When it activates and tries to capture them, Rubes uses his analytical fire control to disable it. The Council examines the drone and suspects Thornok has created an artificial Butterfly Squirrel.
Inside Thornok's laboratory, we meet Baby Pip - a young artificially created Butterfly Squirrel. Despite her confined existence, she's developed bonds with three mechanical caregivers - Whirly, Scrappy, and Morphix - who secretly plan to help her escape.
The Council decides a mission to gather intelligence about Thornok's activities is necessary. Despite concerns about their safety, Pip and Rubes join their parents and friends on this dangerous expedition, as Pip's connection to the mysterious butterfly squirrel grows stronger.
The expedition team begins their journey through the Rainbow Rapids, where they encounter and narrowly escape Thornok's hunter drones. Pip's connection with Baby Pip strengthens, allowing her to receive warnings about threats.
The team camps at the edge of Misty Meridian, where Pip's connection with Baby Pip reveals that her escape attempt is imminent. They decide to take a dangerous shortcut through the Heart of the Meridian to reach her in time.
The team navigates the treacherous Heart of the Meridian with help from mysterious manifestations. They find a direct portal to Thornok's facility and arrive just in time to help Baby Pip escape, though Whirly sacrifices himself in the process.
A week after the rescue, Baby Pip chooses the name Willow and begins adjusting to life in Heart Woods. Rubes creates a Memory Projector that helps her share her experiences, and she discovers her purpose might be to bridge the gap between living beings and mechanicals.