Yomawari 3 focuses on a unnamed girl who had awoken in an unfamiliar dark forest. She has no recollection on how she got there, with her last memories being that she went to the school's rooftop at sunset when the school day was over.

As she wanders around in the dark forest, she cross paths with a strange figure with no form. It claims that the protagonist had been cursed and she needs to remember a forgotten memory in order to break that curse. With no other choice, the girl will explore this haunted town at night in order to find these lost memories in hopes of breaking this curse.