"Armed Girl's Machiavellism" is set in a unique academy where female students are permitted to carry weapons, while male students are subjected to strict disciplinary rules. The story centers on Nomura Fudou, a delinquent transfer student who is forced to enroll at this institution. Upon arrival, he encounters the Five Supreme Swords, a group of powerful female students who enforce the school's rules with martial prowess. Each of the Five Supreme Swords wields a distinct weapon and fighting style, reflecting their personalities and leadership roles within the academy.

Fudou quickly becomes a target of the Five Supreme Swords, particularly their leader, Rin Onigawara, who challenges him to prove his worth. Despite his initial reluctance, Fudou demonstrates exceptional combat skills, earning the respect and curiosity of the group. As the narrative progresses, Fudou's presence disrupts the established order, leading to conflicts, alliances, and personal growth among the characters. His interactions with the Five Supreme Swords reveal their individual struggles, motivations, and vulnerabilities, gradually humanizing them beyond their intimidating reputations.

The series explores themes of power dynamics, gender roles, and personal redemption, as Fudou navigates the academy's rigid hierarchy. His journey involves confronting various adversaries, including rival factions and external threats, while also fostering camaraderie with the Five Supreme Swords. The narrative balances action-packed sequences with moments of humor and introspection, creating a dynamic and engaging storyline. Key characters include Rin Onigawara, the stoic and disciplined leader; Satori Tamaba, the cheerful yet formidable second-in-command; and Warabi Hanasaka, the youngest and most enigmatic member of the group. Each character contributes to the evolving dynamics of the academy, as Fudou's influence challenges their perceptions and reshapes their relationships.