Miyori, an 11-year-old girl, is sent to live with her estranged grandmother in a rural village after her parents' divorce. Struggling with feelings of abandonment and resentment, Miyori finds herself isolated in her new environment. The village is surrounded by a dense forest, known as Miyori's Forest, which is believed to be inhabited by spirits and supernatural beings. Initially dismissive of the local folklore, Miyori soon encounters these spirits herself, including the mischievous fox spirit Kon and the wise, tree-like entity known as the Forest Elder.

As Miyori begins to interact with the spirits, she learns that the forest is under threat from human development. A construction project plans to destroy the forest to build a dam, which would displace the spirits and disrupt the natural balance. The spirits, recognizing Miyori's unique ability to see and communicate with them, ask for her help to protect their home. Reluctant at first, Miyori gradually forms bonds with the spirits and the villagers, finding a sense of belonging she had been missing.

Miyori's journey involves navigating the complexities of human and spirit relationships, as well as confronting her own emotional struggles. She discovers that her grandmother, who initially appears cold and distant, has a deep connection to the forest and its spirits. Through her grandmother's guidance and her own experiences, Miyori begins to understand the importance of preserving the forest and the delicate harmony between humans and nature.

The narrative explores themes of environmental conservation, the impact of human actions on nature, and the healing power of connection and community. Miyori's growth is central to the story, as she transitions from a lonely, resentful child to a determined protector of the forest. The spirits, each with distinct personalities and roles, play a crucial part in her development, offering both challenges and support.

The climax of the story involves a collective effort by Miyori, the villagers, and the spirits to halt the construction project. Through unity and perseverance, they manage to save the forest, ensuring its survival for future generations. The resolution sees Miyori finding peace with her new life, embracing her role as a bridge between the human and spirit worlds, and reconciling with her past. The story concludes with a sense of hope and renewal, emphasizing the enduring bond between humanity and the natural world.