Due to her parents' constant fighting, Yachiko Togakushi has decided to live in a dormitory that has been abandoned for the past five years. Condemned by many, it is believed to be haunted by the Man of the Gaps—a ghost who is said to be always observing the dormitory's residents from tight spaces. Refusing to believe in this senseless rumor, Yachiko begins to settle into her new home despite her friend's warning.

On her first night, Yachiko encounters the Man of the Gaps and learns of his true name, Giko. Previously on a quest for knowledge when he was still alive, Giko lingers to understand the one mystery he could never comprehend throughout his entire life—the heart of a girl. Set on deciphering this enigma, he begins to write the "Girl Dictionary," a compilation of his research.

With Yachiko's help, Giko meets with a variety of girls, each with diverse personalities and backgrounds. As the Girl Dictionary slowly reaches its completion, Yachiko realizes that there lies a bigger question at hand: the origins of Giko himself.