While ostensibly an episodic anthology, Season 1's narrative core turns on Episode 12 ("One-Eyed Fish"), revealing Ginko was born as a boy named Yoki. After a catastrophic landslide kills his mother, Yoki is taken in by Nui, a grieving Mushi-shi who has lost her family to the pond-dwelling Tokoyami (living darkness). When Nui is fully consumed by the void, Yoki tries to save her and is engulfed, losing his left eye. To survive, he accepts the light of the luminous Ginko Mushi, which erases his memories, bleaches his hair white, turns his remaining eye green, and curses his body to perpetually attract Mushi. Waking with amnesia, he names himself "Ginko" after the creature.
In Season 2, Ginko's visits with Tanyū Karibusa highlight the heavy cost of the hereditary Black Mushi sealed within her body. The special "Path of Thorns" exposes human hubris as the Minai clan fails to domesticate dangerous Mushi rifts, proving primordial forces cannot be subjugated for utilitarian motives.
The narrative reaches its ultimate conclusion in Suzu no Shizuku. A girl named Kaya is transmuted by a bell-like Mushi to become the mountain lord's successor. Ginko intervenes to stop her family from violently rescuing her, allowing Kaya to surrender her human identity to sustain the mountain ecosystem. The saga ends without romance or combat, concluding with Ginko picking up his medicine box and walking down another dirt trail as a solitary, eternal custodian of life.