When Kanako Miyamae transferred to a new all-girls school, she hoped to find true love. Instead, she encountered the beautiful Mariya Shidou, a charming classmate she met on her first day. However, Mariya has one flaw: he is actually a cross-dressing boy! After discovering Mariya's secret and becoming stuck with him as her roommate, Kanako's life has turned into a series of misfortunes. All she wants is to find the girl of her dreams, which is difficult given the meddling of the sadistic Mariya and his sharp-tongued maid, Matsurika Shinouji. Maria†Holic Alive continues Kanako's story as she deals with being Mariya's roommate and aims to find true love, while enduring high school itself.