Thirteen girls, each with the ability to materialize "Elements" and summon metallic guardians called "Childs" have been brought to Fuuka Academy to battle mysterious creatures called Orphans. Each with a different personality and background, they must decide who they truly care about and why they fight.

Kannazuki no Miko begins in the village of Mahoroba, where time passes slowly for both man and nature. Two students from the village's prestigious Ototachibana Academy might as well be night and day. Himeko is shy and unassertive, while Chikane is bold and elegant. Despite this, they love each other, and nothing can come between them, no matter how hard they try. On the two girls' shared birthday, a sinister voice corrupts one of their friends into attacking them, and just when it seemed grimmest, the lunar and solar priestess powers that lay dormant in the two girls awaken, dispelling the evil. That was only the first hurdle, however. The two must now fend off the countless others who would threaten their well-being—even the people closest to them!

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. Aer 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. (Source: Media Blasters)