The story of Qwaser of Stigmata focuses on two high school kids named Mafuyu Oribe and Tomo Yamanobe. They both attend the St. Mihailov Academy where they have been tortured by their other classmates that follow direct orders from the daughter of the dean, Miyuri Tsujidou, as well as her right-hand woman and second-in-command, Hana Katsuragi. One day, Tomo and Mafuyu's lives turn upside-down as soon as the meet a russian nurse named Alexander 'Sasha' Nikolaevich.