The movie adapts a story from volume 5 of the Kino's Journey light novel series: Kino travels to a country divided into two parts: the very clean and peaceful city, closed off from the surrounding wastelands. Kino meets a little girl in the city suffering from a disease which is constantly being researched. The girl, however, does not know just how the research is being done.

In this prequel to the Kino no Tabi series, young Kino is being trained by her teacher. She learns how to ride her motorrad Hermes and develops her gift of excellent marksmanship. However, her guilt concerning the real Kino is with her when she decides to set off on a journey. All the while, Kino is becoming confused about her real identity.