Shinobu is a high school girl who insists she is completely ordinary, yet she is frequently seen scaling walls, throwing shuriken, and disappearing in clouds of smoke. Her classmate, the diligent Hitoyoshi Kageyama, is the only one who witnesses these acts and remains thoroughly unconvinced by her denials. While she is a highly skilled ninja in truth, Shinobu is utterly inexperienced with normal social interactions, particularly friendship and romance. This creates the central dilemma of her life: she wishes to be seen as an average girl so she can grow closer to Hitoyoshi, but her ninja habits and his persistent suspicions constantly complicate her efforts.

The story unfolds in a contemporary Japanese town where Shinobu navigates the familiar landscape of a romantic comedy, from school festivals and sports days to summer festivals. Despite her prowess in combat and infiltration, she is clumsy and tongue-tied when trying to express her feelings. Hitoyoshi, for his part, is dependable but dense, initially viewing her more as a mysterious ninja to be observed than a potential love interest. As they participate in various school activities, the two gradually close the distance between them. Shinobu begins to experience the joys of friendship with her female classmates and the struggles of trying to impress her crush, all while trying to suppress her ninja instincts.

A key narrative arc explores the difference between Shinobu's obsessive, stalker-like attention and a genuine, reciprocal relationship. Her journey of emotional growth is contrasted with her backstory, which reveals she was once completely detached from society, caring only about her ninja duties before Hitoyoshi reached out to her. Supporting characters, including a tomboy little sister, a popular wingman friend, and a childhood friend named Kazumi, help create a wholesome and low-drama environment. Kazumi, in particular, presents an interesting parallel to Shinobu, as she values her friendship with Hitoyoshi over forcing a romantic angle, highlighting the different forms connection can take. Through these interactions, the series focuses on Shinobu’s transformation from a secluded operative into a high school girl learning to open her heart.