Fumio Shijō is the central character in the story of Arch Angels. Following the death of her mother, she meets her brother, Kazuomi Shijō, for the first time. Nicknamed "the prince," he enrolls her at St. Michael's Academy, an elite school located on a remote island designed to shelter young women from worldly temptations. The academy's environment, where all students are expected to be angelic, beautiful, courteous, innocent, and modest, is a poor fit for Fumio, who feels deeply uncomfortable and struggles to play the role of a "well-bred young lady". Her personal preferences and desires are much more ordinary; her true wish is to attend Tokyo University and enjoy simple, everyday food like junk food.

Fumio's personality is defined by this clash between the stifling expectations of her new life and her own down-to-earth nature. She finds the school's atmosphere to be "hell on Earth" due to its focus on class, elegance, and refined tastes. In a moment of rebellion against the constraints placed upon her, she follows her instincts and skips class to go eat a bowl of chicken ramen. This act of defiance is a key demonstration of her core motivation: the desire to be true to herself, even when it defies the strict social code of St. Michael's. When confronted by her classmates, she confesses her "commoner" side, revealing her honesty and her lack of pretense.

Fumio's primary role in the story is as the reluctant heroine who, through her authenticity, forms a crucial friendship. After she admits her true nature, her class president, Kazuna Saiki, and vice-president, Yuzuko Sarashina, reciprocate by confessing their own hidden, less-than-angelic interests, such as enjoying trashy novels. Kazuna and Yuzuko become her kindred spirits, and it is this growing bond of friendship that forms the emotional core of the narrative. Her relationship with her brother, Kazuomi, is the catalyst that places her at the academy, but it is the connection with her two female peers that empowers her. As their friendship develops, a series of mysterious kidnappings of "well-bred young ladies" begin to threaten the school. This event forces Fumio and her new friends to move beyond simply coping with academy life and take on a more active role.

Fumio undergoes significant development from a girl who feels out of place and resorts to hiding her true self, to a young woman who finds allies in her peers and ultimately gains the agency to defend her school. The strange incident that occurs when she is found by Kazuna and Yuzuko skipping class appears to be a turning point that leads to the trio awakening notable abilities. Fumio, along with Kazuna and Yuzuko, gains superpowers. These abilities, which seem to manifest in connection with their genuine friendship, equip them to track down the villains, who are described as Italian kidnappers or pirates, and bring them to justice, defending their isolated academy from the threat.