"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 operates under a unique mentorship system called the "sœur" (sister) system. Upperclassmen, referred to as "soeurs," take on younger students as their "petites soeurs," guiding them through school life and fostering close, often deeply emotional bonds.

The narrative begins with Yumi Fukuzawa, a first-year student who is unexpectedly chosen as the petite soeur 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 being her soeur, gradually grows into her role, navigating the complexities of their relationship and the expectations of the school's traditions. 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 soeur of Sei. The relationships between these characters are central to the story, with themes of loyalty, love, and personal growth woven throughout. The soeur system serves as a framework for examining the emotional and social dynamics of adolescence, as the characters confront their insecurities, aspirations, and the challenges of maintaining meaningful connections.

As the story progresses, Yumi and Sachiko's bond deepens, and Yumi becomes more confident in her role within the Yamayuri Council. The series also delves into the histories of other characters, such as Yoshino Shimazu and Rei Hasekura, whose relationship as soeurs is tested by personal conflicts and misunderstandings. The narrative balances lighthearted moments with more serious themes, including the pressures of societal expectations and the search for identity.

"Maria-sama ga Miteru" is characterized by its focus on character development and interpersonal relationships, with the school setting providing a backdrop for exploring the nuances of human connection. The series avoids overt melodrama, instead opting for a subtle and introspective approach to storytelling. The manga captures the quiet intensity of its characters' emotions, offering a thoughtful portrayal of the bonds that form within the unique environment of Lillian Girls' Academy.