Root Letter is set in Matsue, Shimane Prefecture, where the protagonist arrives in search of Fumino Aya, a pen pal friend from high school who had disappeared for 15 years. After he finds a letter dedicated to him from her that was never sent, he sets out to interrogate her classmates as he wonders if everything Aya had told him had been a lie. The game contains multiple endings based on the player's choices throughout the game.