"Maria-sama ga Miteru" is a manga series set in the prestigious Lillian Girls' Academy, a Catholic all-girls school in Tokyo. The story revolves around the relationships and dynamics within the school's student council, known as the Yamayuri Council, which is deeply rooted in a tradition of mentorship called the "sœur" system. This system pairs older students (the "grande sœurs") with younger ones (the "petite sœurs") in a bond of guidance and friendship, symbolized by the exchange of rosaries.

The narrative begins with Yumi Fukuzawa, a first-year student who is unexpectedly chosen as the petite sœur of Sachiko Ogasawara, a refined and elegant third-year student and a member of the Yamayuri Council. Yumi, initially overwhelmed by Sachiko's grace and the responsibilities of the sœur system, gradually grows into her role, navigating the complexities of school life, personal insecurities, and the expectations placed upon her. Sachiko, though initially distant and reserved, begins to open up to Yumi, revealing her own vulnerabilities and struggles.

The series explores the lives of other members of the Yamayuri Council, including Sei Satou, a charismatic and enigmatic figure with a mysterious past, and Shimako Toudou, a quiet and introspective student who becomes the petite sœur of Sei. The relationships between these characters are central to the story, as they navigate themes of loyalty, identity, and the evolving nature of their bonds. The sœur system, while fostering deep connections, also creates tensions and rivalries, particularly as new students enter the academy and vie for the attention of the grande sœurs.

As the story progresses, the characters face various challenges, both personal and interpersonal. Yumi's journey is marked by her efforts to understand Sachiko's aloofness and to prove herself worthy of their relationship. Sachiko, in turn, grapples with her own expectations and the pressure of upholding her family's legacy. Sei's past and her relationship with Shimako add layers of complexity, as Shimako struggles to reconcile her feelings with her sense of duty. The series also delves into the lives of other students, such as Yoshino Shimazu and Rei Hasekura, whose own sœur relationship is tested by misunderstandings and external pressures.

The narrative is structured around the school year, with key events such as the school festival, Christmas celebrations, and graduation ceremonies serving as backdrops for character development and emotional moments. The series balances lighthearted, slice-of-life moments with deeper explorations of the characters' inner lives, creating a rich tapestry of relationships and experiences. Through its focus on the sœur system and the bonds it creates, "Maria-sama ga Miteru" offers a nuanced portrayal of friendship, mentorship, and the challenges of growing up in a tightly-knit community.