Clover Reset begins at Shonan Saika Academy, an all-girls institution in Kanagawa Prefecture, ushering in a period of change for its students. Marin Tachibana, along with her friends Mashiro Saotome and Kiyoka Jinguji, experience a momentous day that redirects their routine. The day begins with the arrival of Shizuku Kujou, a new student who displays an outwardly composed and reserved personality. For Marin, meeting Shizuku for the first time feels like an old acquaintance.