The students of the Barsburg Empire's Military Academy are trained to become capable fighters who will serve as the empire's newest soldiers. Every year, five hundred students take a graduation exam, where only 20 can pass to become honorable "begleiters," a position equivalent to assistant executive officers. Students fight their enemies by using "zaiphon," God-given abilities that take different forms depending on the individual.

Teito Klein, the academy chairman's favorite student, is belittled by his peers due to his previous status as a slave. Despite being unable to fully remember his past, Teito's cheerful best friend, Mikage Celestine, stays by his side. After the two undergo the exam, Teito recalls small pieces of a long-forgotten memory, causing him to instinctively attack the chief-of-staff, Ayanami.

Subdued for his insubordination, Teito is imprisoned for further questioning. But with the help of Mikage, Teito escapes to the Barsburg Church in the empire's Seventh District. As he struggles to escape the clutches of the Barsburg Empire's military, he unveils the memories that lie within him and learns about a compelling power that roams in the shadows of the empire.

Included one-shot: Volume 17: Seven Ghosts (pilot)