"Kinokoinu - Mushroom Pup" is a fantasy-adventure anime centered around a young, anthropomorphic mushroom dog named Kinokoinu, who embarks on a journey to save his forest home from a mysterious blight. The story begins in the tranquil Mushroom Forest, where Kinokoinu lives peacefully with other magical creatures. However, the forest begins to wither as an unknown corruption spreads, threatening the lives of its inhabitants. Guided by an ancient prophecy, Kinokoinu sets out to find the legendary "Golden Spore," a mythical artifact said to purify the land and restore balance.

Along the way, Kinokoinu encounters a diverse cast of characters, each with their own motivations and connections to the forest's plight. Among them is Tama, a mischievous but loyal firefly who becomes Kinokoinu's guide and companion. Together, they navigate treacherous landscapes, including the toxic Swamp of Decay and the perilous Crystal Caverns, while facing adversaries such as the Blight Wraiths, shadowy entities born from the corruption. The duo also meets allies like Shii, a wise but reclusive mushroom elder, and Kumo, a spider weaver with knowledge of the forest's ancient secrets.

As the journey progresses, Kinokoinu learns about the origins of the blight, which is tied to a forgotten conflict between the forest's guardians and a vengeful spirit. The narrative explores themes of environmental preservation, resilience, and the interconnectedness of life. The climax unfolds in the heart of the forest, where Kinokoinu must confront the spirit and make a pivotal choice to either destroy the blight at great personal cost or find a way to heal both the forest and the spirit. The resolution emphasizes the importance of harmony and understanding, leaving the forest's future open to renewal and growth.