The story follows Takao Kasuga, a bookworm whose favorite book is Charles Baudelaire's Les fleurs du mal, after which the series is named. One day after school, he discovers and impulsively steals the gym clothes of Nanako Saeki, the classmate he has a crush on. However, a lonely girl named Sawa Nakamura happens to catch him in the act. Nakamura blackmails Kasuga into a "contract," or else she will reveal his secret.