"Jeremy no Ki" centers around Jeremy, a young boy living in a rural village surrounded by a mystical forest. The forest is home to ancient trees believed to possess spirits, and Jeremy develops a unique connection with one of these trees, which he names "Ki." The tree begins to communicate with him, revealing that it is a guardian spirit tasked with maintaining the balance between nature and humanity. However, this balance is threatened by an encroaching industrial force seeking to exploit the forest's resources.

As Jeremy grows closer to Ki, he learns about the forest's history and the spirits' role in protecting it. The narrative explores themes of environmentalism, coexistence, and the consequences of human greed. Jeremy becomes determined to save the forest, but his efforts are met with resistance from both the industrial developers and some villagers who see the forest's destruction as a path to economic prosperity.

Key characters include Jeremy's childhood friend, Aya, who supports his mission but struggles with her own fears about the future. There is also Old Man Haruto, a village elder who holds knowledge of the forest's secrets and serves as a mentor to Jeremy. On the opposing side, the industrial developer, Mr. Kuroda, represents the forces of modernization and exploitation, driven by profit rather than respect for nature.

The story unfolds through Jeremy's journey to unite the villagers and the forest spirits against the industrial threat. Along the way, he faces moral dilemmas, personal growth, and the challenge of bridging the gap between human ambition and environmental preservation. The narrative builds toward a climactic confrontation where Jeremy must rely on his bond with Ki and the collective strength of the community to protect the forest and its spirits. The series balances moments of tension and action with quieter, reflective scenes that highlight the interconnectedness of all living things.