The human race has been hunted to near extinction, leaving the world ridden with all sorts of curious and mysterious creatures. In the middle of a forest, a lone Golem comes across "it": a dishevelled human dressed in rags and bound by chains.

Taking the child in, the Golem comes to learn that the child is called Somali, and that she has no recollection of her parents. Spending time together, the two grow to share a bond akin to a father and daughter. The Golem decides to leave behind his obligation as the Guardian of the Forest in pursuit of Somali's parents or, at the very least, any other remaining humans. To Somali, her parents are the least of her worries—she believes she already has the only parent she needs.

Somali to Mori no Kamisama depicts the journey Somali and the Golem undertake in order to seek out other humans, all while keeping Somali's identity hidden for her safety.