The story follows the travels of Hazuki Azuma, a tall, brooding high-school girl, as she searches for her adopted older sister and love interest, Hatsumi, in many different "book worlds". Her search is rather more of a focus in the anime series, in which Hazuki is the main character, than in the game. The main character of the game, the player, is nameless and occupies a different body in different "book worlds", including Hazuki's at some points. After the disappearance of her sister in the anime, a talking parakeet nicknamed Ken-chan introduces Hazuki to another major character of the series; Lilith, the caretaker of the Great Library. Each book in the library contains a different world, and the guardian of the library takes on the title Yami. As Yami, Lilith wears an enormous single-eyed hat. In the game, the main character's constant companion is Ken-chan. The anime is an attempt to bridge the gap between shōjo and shōnen anime; without the fan service, the series could be considered a shōjo anime, since it is mostly character-driven and focused upon developing relationships. For this reason, as well as the fact that most of the female characters seem to be attracted to Hazuki, the anime series is popular among yuri fans.
The anime is sometimes criticized as being difficult to follow, due to its non-linear plot and self-referential nature. For example, the first episode of the anime jumps ahead to after Hazuki has met Lilith, however their actual meeting and explanation of how they get to each book is not shown until later. The anime is narrated by Arya, and the common visual aid to understanding the jumps is to imagine him sitting in a messy pile of books picking one at random to read to you.