Kyotaro Kakei has always had an affinity towards books in hopes to find answers to his life. With a mentor's promise, he continues to search for a book with his absolute hope. However, this changes when he receives a foretelling message saying that "Today, something will happen that will change your fate. --From the Shepherd." Due to this premonition, his normal school life at Shiomoi Academy becomes entangled due to the optimistic Tsugumi Shirasaki and the Shimoi Happy Project.

Bottle Fairy follows a quartet of cute fairies as they play, study, and learn (often incorrect) lessons about the human world.

Tsutsui Hikari (a.k.a "Tsuttsun") is a high school student who is content with his virtual life of anime and video games. One day, he gets stuck cleaning the pool with Iroha, a real live girl who is stylish, sassy and known to be easy with boys ... and she aggressively approaches him! Tsuttsun, who has few friends and lives in his own world, finds himself smitten by the confident and wild Iroha ... and his whole world is turned upside down!! It's the awkward and pure love story of a boy who experiences relationship for the first time.

One day, high-school boy Yamada bumps into the beautiful girl Shiraishi on the stairs (literally), and their lips touch as they fall. When they regain their wits, they realize that they have swapped bodies. As time progresses, the two realize that this is not the only mysterious happening in the school.