"Only the Flower Knows" is a manga series that explores themes of love, identity, and self-discovery through the lens of a supernatural premise. The story centers on Rintarou Takiya, a reserved and introverted college student who struggles with feelings of isolation and a lack of direction in life. One day, while visiting a botanical garden, he encounters a mysterious flower that grants him the ability to switch genders. This transformation occurs unpredictably, leaving Rintarou to navigate the complexities of living in two different identities.

As Rintarou adjusts to this dual existence, he meets Yuu Sonoda, a cheerful and outgoing classmate who becomes intrigued by Rintarou's enigmatic behavior. Yuu is unaware of Rintarou's secret but is drawn to his quiet demeanor and begins to form a close bond with him. Over time, their relationship deepens, and Rintarou finds himself grappling with his feelings for Yuu while struggling to reconcile his dual identity. The story delves into Rintarou's internal conflict as he questions his sense of self and the nature of his connection to Yuu.

The narrative also explores the societal expectations and pressures surrounding gender and relationships, as Rintarou's experiences in both male and female forms provide contrasting perspectives on how he is perceived and treated by others. The flower's power serves as a metaphor for the fluidity of identity and the challenges of understanding oneself in a world that often demands conformity.

Throughout the series, the relationship between Rintarou and Yuu evolves, with moments of tenderness, confusion, and emotional vulnerability. The story balances its supernatural elements with a grounded exploration of human emotions, focusing on the characters' growth and the deepening bond between them. The manga ultimately examines themes of acceptance, love, and the courage to embrace one's true self, even in the face of uncertainty and societal norms.