Shiomi Academy, an elite high school, boasts a student body of 50,000 and is home to the Shiomi Daitoshokan (Great Library). It also has a famous urban legend: a mysterious figure called "The Shepherd," who appears before hard working students to grant them a wish.

Kyotarou Kakei is a second year of Shiomi Academy, and loves to read more than anything else. Other than when he's in class, his nose is pretty much always in a book in the Daitoshokan. His dream is to spread his love of reading through the Library Club.

One morning Kyotarou gets a strange email from 'The Shepherd' which tells him that something is going to happen to him which will change his fate. This triggers a sense of foreboding within him that causes him to rush back to the train platform and save another student, Tsugumi Shirasaki, from getting killed by a derailment. After a string of misunderstandings though, Kyotarou finds himself with three new members joining his library club while also becoming involved with Tsugumi's "Happy Project."

The questions remain though; what is Tsugumi's "Happy Project"? Who is this mysterious Shepherd who keeps sending them emails? The school year is about to get a whole lot more interesting for Kyotarou and his new friends.