|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.
Sora soon learns why Sunao identified himself as "Ran" that first night: he and Sora have alternate personalities. Sora's is Yoru, a powerful protector and the lover of the more dependent, feminized Ran. The existence of these alternate personalities, and the relationship between them, has some mysterious connection with Sora's fall from the window and his forgotten past. The alternate personalities' passionate relationship is a far cry from the hostility and distrust between Sora and Sunao. Because Yoru and Ran possess them arbitrarily, Sora and Sunao frequently find themselves in embarrassing situations when they regain control of their minds.
Other comical situations arise from Matsuri's efforts to draw Sora and Sunao into his moneymaking schemes, known as the group "The School Do-It-Alls" and from such minor characters as a bishōnen ghost and three younger boys who resemble the trio. No parents are ever mentioned, and the only authority figures are school nurse Kai Nanami and math teacher Shinichirou Minato, but it is known that Sora and Sunao are both orphans. Both have some connection with Sora and Sunao's dark past, which also involves one of the older students at the school, Kai Nagase, and a mysterious doctor named Aizawa.