In a small, suffocating Japanese town in 1998, middle school student Takao Kasuga is a quiet bookworm who feels alienated from his classmates. His only escape is the poetry of Charles Baudelaire, particularly the collection The Flowers of Evil, which he believes articulates the darkness and yearning he feels inside. He secretly idolizes his classmate Nanako Saeki, seeing her as the embodiment of an unattainable, pure ideal.

One afternoon, acting on a sudden, unexplainable impulse, Takao steals Nanako’s gym clothes. He is not caught by a teacher, but by a strange, volatile girl named Sawa Nakamura. The class outcast with a wild look in her eyes, Nakamura is fascinated by Takao’s transgression. Instead of reporting him, she forces him into a contract, becoming his blackmailer and self-appointed master. She will keep his secret, but only if he agrees to expose the rotten, perverse side of himself that he tries so hard to hide.

Caught in Nakamura’s sadistic grip, Takao’s life spirals into chaos. He is forced to act out increasingly destructive and humiliating scenarios designed to tear down his facade of normalcy. Simultaneously, to his own astonishment, he begins a tentative, innocent relationship with Nanako, who is drawn to his mysterious and melancholic air. Trapped between the angelic girl who represents a conventional future he feels he doesn't deserve and the demonic girl who demands he confront his ugliest inner self, Takao is torn apart. His guilt over his initial crime festers as Nakamura pushes him to commit even worse acts. The conflict barrels toward a breaking point at the local town festival, where all pretense is stripped away, forcing a public and irreversible confrontation with the flowers of evil blooming within them all.