Due to hunting, the human population has been reduced to a point where the world is now home to peculiar and enigmatic creatures. In the midst of a forest, a solitary Golem encounters a disheveled human, dressed in tattered clothes and shackled with chains.
After taking the youngster under its care, the Golem discovers that her name is Somali, and she cannot recall anything about her parents. Spending time together, the two develop a rapport that resembles a father-daughter bond. The Golem relinquishes its Forest Guardian duties to locate Somali's parents or any surviving humans. However, Somali is more concerned about her relationship with the Golem and does not consider finding her parents necessary.
Somali to Mori no Kamisama chronicles the journey of Somali and the Golem as they embark on an expedition in search of other humans while shielding Somali's true identity to ensure her safety.