AD 2300, the human race has advanced to space, and a lot of planetary nations have been founded. Amaterasu is a newly built space battleship of a planetary nation, Kibi. It is operated by apprentice officers of Defense Academy. When it is about to return from the test flight, the Alliance of Henrietta Nations declares war against Kibi. The alliance destroys the battleships of Kibi by its overwhelming military power, and Kibi surrenders to the alliance. However, the apprentice officers in Amaterasu don't want to surrender without fighting. In order to fight against the alliance, they come up with an idea. They ask Galaxy Network, a galaxy wide TV network, to become their sponsor. In return for receiving money, they let Galaxy Network broadcast their war. Amaterasu and Galaxy Network, being involved various speculations, a solitary war of Amaterasu begins.
The Ukishima sanctuary is located in a picturesque old town on the edge of a lake. Saya Kisaragi, a young priestess of the temple lives there with her father, Tadayoshi. During the day, she lives the life of a normal high school student at the Sanbar academy. But at night, she hunts the "Ancient", creatures possessing supernatural physical abilities who prey humans and which alone she has the ability to defeat.
A dream of falling from the sky...and then birth. Rakka is born from a large cocoon into the Old Home, greeted by a group of females with small wings on their backs and shining halos above their heads. Soon Rakka's own wings grow, a halo is placed on her head and she is told that she must work in the nearby town of Grie. She soon realizes that the town and the entire world they live in are confined behind the Wall, a tall, impenetrable wall that none except the mysterious Toga are allowed to exit.