It has been half a decade since Utena Tenjou's parents passed away. However, instead of mourning, Utena vividly remembers the mysterious prince who comforted her in her time of need. That day, the prince—whom she nicknames "Peropero-kun" after he licks her tears away—bestowed upon her a ring and promised that as long as she possesses the keepsake, it would lead her back to him one day.

Since then, Peropero-kun sends Utena a letter once a year just as the roses begin to bloom. Believing the letters are written by Utena's aunt rather than an obscure nobleman, Utena's best friend Kaidou decides to search for evidence that supports his suspicions. When he finds six photos that connect like puzzle pieces in the letters, it proves that not only does Peropero-kun exist, but also that he can be found at the prestigious Ohtori Academy.

Wishing to reunite with her long-lost prince, Utena leaves her current life behind to embark on her search for Peropero-kun. After arriving at the academy, she encounters the Ohtori Academy's student council and their strange treatment of fellow student Anthy Himemiya. Utena's investigation into this shady behavior unleashes a plethora of mysteries that may just lead her to the prince she has sought for so long.