Goshūshō-sama Ninomiya-kun's story revolves around Shungo Ninomiya, a male high school student trained in difficult hand-to-hand combat. He lives in a huge house with his older sister Ryōko, who is almost always gone on some dangerous mercenary mission. One day, his sister sends Mayu and Mikihiro Tsukimura, two siblings, to live with him to help Mayu overcome her fear of men. Unfortunately this is accomplished by making Mayu and Shungo share the same room and even sleep together in the same bed. Making things even worse, Reika Hōjō, the student-council chair, is blackmailed into becoming their maid due to a video that Ryoko recorded, in which she tries to seduce Shungo.