Rinichi Sagara is a middle school student troubled by his short stature and feminine features. His sensitivity about his appearance often provokes him into fights, earning him a reputation as surly and intimidating. Most classmates avoid him, except for the kind Aya Kurokawa, whom he secretly likes, and Yuu Narumi, his rival for Kurokawa's affection. One day, while arguing with Narumi, Sagara collapses. When he regains consciousness, he discovers he has transformed into a girl.

This sudden change is the result of a phenomenon called emergence, a biological mechanism that randomly alters some boys into girls to maintain an equal male-to-female ratio in the population. Sagara refuses to accept his new body and becomes even more determined to act masculine. However, both Kurokawa and Narumi soon learn his secret, upsetting the previous dynamic of their love triangle. The story follows Sagara's struggle with his identity, his relationships, and his attempts to navigate school life while hiding or confronting his transformation.

The manga is structured as a series of volumes, each containing distinct narrative arcs. The first volume features Mamiya and Miyoshi from the original Kanojo ni Naru Hi series, revisiting them five years after the events of that story. The second volume includes a separate one-shot titled S no Kaikoroku (Memoirs of a Sadist), which follows a character named Natsukawa as he becomes gradually drawn into a dangerous S&M relationship with his girlfriend Sakurai. The fourth volume concludes with a set of four-panel comics and a brief epilogue set shortly after Sagara first began living as a girl.