Hiro Hiyorimi is a boy who has just moved to the city to meet his sister. While walking down the sidewalk, he is suddenly hit by a car (crushed by construction beams in the anime). On the verge of death, he is seen by a young woman clad in gothic clothes. She then resurrects him, leaving him alive in the hospital morgue. He wakes up confused over what happened, only to encounter the woman again as she eliminates some wolf creatures. She addresses Hiro as "her servant" and introduces herself as "Hime" (Japanese for Princess). The story then follows Hiro as he assists Hime in killing creatures that have been sent by her siblings to attack her.
In the peaceful theocracy of Simulicram, everyone is born female. At age 17, each maiden undergoes a special ceremony where she chooses her sex. However, only Pairs of maiden priestesses can synchronize with the ancient flying ships known as Simoun needed to defend Simulicram. These Pairs refrain from undergoing the ceremony as long as they wish to keep piloting their Simoun. Aeru is recruited to be a Simoun pilot after a terrifying attack by an enemy nation decimates the squadron known as Chor Tempest. To earn her wings she needs to find her way into the heart of Neviril, Regina of Chor Tempest. But Neviril s heart still belongs to her previous Pair, lost in the battle when she attempted a forbidden Simoun maneuver.