Da Capo II takes place 53 years after the events of Da Capo, when Sakura Yoshino, weary of being alone for so long, wished upon a prototype artificial wish-granting magical cherry tree for a son—Yoshiyuki Sakurai. In the first arc, while Yoshiyuki attends Kazami Academy, beneath the school, he awakens Minatsu Amakase, a robot. Yoshiyuki helps her adapt to a life with humans despite robots being nothing more than mere tools. In the second arc, Yoshiyuki begins to harbor feelings for his stepsisters, Otome and Yume, the granddaughters of Jun'ichi and Nemu. However, the cherry tree starts malfunctioning, granting all wishes, regardless of how impure, which is causing numerous incidents to occur in Hatsune. The situation gradually worsens and Otome has to choose whether or not to wither the cherry tree, which would erase Yoshiyuki's existence in the process, so as to save Hatsune.