High-school student Sora Hashiba was hospitalized after falling from the fourth floor of the school building. On his first night back in the dormitory, he wakes to find a strange boy addressing him by the name "Yoru". The stranger identifies himself as "Ran" and says he's Sora's new roommate. The next day, Sora's childhood friend and dorm manager, Matsuri Honjou, informs Sora that the other boy, whom Matsuri identifies as Sunao Fujimori or "Nao-kun," is actually another childhood friend of Sora. Sora doesn't remember meeting Sunao before. In fact, Sora can't remember much of anything regarding his past, and the series follows his quest to regain his memory.