"Simoun" is set in a fictional world where the nation of Simulacrum is engaged in a prolonged war against neighboring countries. The story unfolds in a society where all individuals are born female and must choose their permanent gender at the age of 17. The series centers on the Simoun, sacred aircraft that can only be piloted by young women known as "Sibyllae." These Sibyllae are revered for their ability to perform powerful maneuvers called "Ri Mājon," which are believed to hold mystical significance and are crucial to the war effort.

The narrative primarily follows a group of Sibyllae from the Chor Tempest, a prestigious Simoun squadron. Among them is Aeru, a reluctant and inexperienced pilot who struggles with her role and the expectations placed upon her. Neviril, the squadron's star pilot and Aeru's partner, serves as a mentor figure but harbors her own emotional conflicts. Other key characters include Paraietta, a determined and skilled pilot, and Dominūra, a mysterious and aloof figure with a complex past. The dynamics within the squadron are shaped by their individual struggles, relationships, and the pressures of war.

As the war intensifies, the Chor Tempest faces increasing challenges, both on the battlefield and within their ranks. The series explores themes of identity, choice, and the consequences of war, as the characters grapple with their impending decision to choose their gender and the implications it holds for their futures. The narrative delves into the emotional and psychological toll of their roles as Sibyllae, as well as the broader societal and cultural significance of the Simoun and Ri Mājon.

The story builds toward a climactic confrontation that forces the characters to confront their fears, desires, and the realities of their world. Through its exploration of gender, identity, and the human cost of conflict, "Simoun" presents a thought-provoking and emotionally resonant narrative that remains a distinctive entry in the mecha and drama genres.