As Sakuta Azusagawa waits for Mai Sakurajima at the beach on her high school graduation day, he encounters a version of Mai from her child acting days. However, when Mai finally arrives, her younger self disappears, leaving him confused. Sakuta spots an unfamiliar scar on his body when he returns home, which confirms his suspicion—he is involved in another case of the inexplicable Puberty Syndrome.

Not long after, Sakuta and his sister, Kaede, receive a call from their father. He tells them that their mother, who had been recently discharged from the hospital, wants to see her daughter once more. Experiencing strange occurrences while visiting his mother with Kaede, Sakuta must find a way to solve the Puberty Syndrome abnormalities.