At Shiomi Academy, a prestigious school with a massive student population and the renowned Great Library, whispers circulate about a shadowy entity known as 'The Shepherd' granting wishes to diligent students. Kyotarou Kakei, a book enthusiast in his second year, is devoted to the library except during classes. Unexpectedly contacted by 'The Shepherd,' Kyotarou's life takes a mysterious turn, leading him to rescue a fellow student from a tragic accident. Through a series of unexpected events and the initiation of Tsugumi Shirasaki's enigmatic 'Happy Project,' Kyotarou finds himself with new additions to his library club. As the secrets of the 'Happy Project' and the true identity of 'The Shepherd' unravel, Kyotarou and his newfound companions brace for a captivating journey in the upcoming school year.