"My-Otome" is set in a fictional world where young women are trained to become Otomes, elite warriors who serve as protectors and guardians to their masters. These Otomes are bound to their masters through a system of contracts and wield powerful abilities derived from their GEMs, special stones that grant them enhanced strength, agility, and combat skills. The story primarily takes place in the kingdom of Windbloom, a nation that relies on the Otome system for defense and diplomacy.

The protagonist, Arika Yumemiya, is a spirited and determined girl from a remote village who travels to Windbloom with the goal of becoming an Otome. She carries a pendant left by her mother, which she believes holds the key to her identity and destiny. Upon arriving at Garderobe Academy, the prestigious institution where Otomes are trained, Arika discovers that her pendant is a rare and powerful GEM, marking her as a candidate for the prestigious role of the "Pearl Otome." However, her lack of refinement and impulsive nature often put her at odds with the academy's strict hierarchy and traditions.

Arika's journey intertwines with that of Nina Wáng, a talented and disciplined student who harbors a deep admiration for Mashiro Blan de Windbloom, the princess of Windbloom and a key figure in the political landscape. Nina's loyalty to Mashiro and her own insecurities create a complex dynamic between her and Arika, as the two girls navigate their rivalry and eventual friendship. Mashiro, meanwhile, struggles with her responsibilities as a ruler and her desire to protect her kingdom from external threats, including the neighboring nation of Aries and its ambitious leader, Sergay Wáng.

As the story progresses, Arika and her peers uncover a conspiracy involving the origins of the Otome system and the true nature of their GEMs. The narrative explores themes of identity, loyalty, and the consequences of power, as the characters confront their pasts and the roles they are destined to play. Key figures such as Erstin Ho, a kind-hearted classmate, and Shizuru Viola, a mysterious and powerful Otome, contribute to the unfolding drama, adding layers of intrigue and emotional depth.

The plot builds toward a climactic conflict that challenges the very foundations of the Otome system, forcing Arika and her allies to make difficult choices about their futures. The series balances action, political intrigue, and character development, creating a rich and engaging narrative that explores the complexities of duty and personal ambition in a world where power and responsibility are inextricably linked.