In Simulicram, a peaceful theocracy, all are born female and at the age of 17, each maiden undergoes a ceremony to choose their gender. However, to operate the ancient flying ships called Simoun that defend their land, only pairs of maiden priestesses can synchronize. These pairs abstain from the gender ceremony to continue piloting. After an enemy nation attacks and destroys the Chor Tempest squadron, Aer is recruited to become a Simoun pilot. In order to earn her wings, she must win the heart of Neviril, the Regina of Chor Tempest. But her heart still mourns her previous pair who was lost during a forbidden Simoun maneuver in battle.