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Teito Klein is a former slave who now attends the Barsburg Empire's military academy due to his ability to use Zaiphon, a type of supernatural power. The ability is rare and thus highly prized. Teito is an amnesiac and doesn't remember anything of his past, but he has recurring and often traumatizing dreams in which he sees a grand church or castle and a familiar but unknown man.

After a year at the academy, Teito prepares to take the notoriously difficult graduation exam. The night before the exam, Teito and his best (and only) friend, Mikage, swear they will never abandon each other if either needs help. Both of them pass the exam. The next day, Teito hears people talking about him; stopping to listen, he suddenly realizes that the speaker, Chief of Staff Ayanami, is the person who killed the familiar man in his dreams, who is his father and the king of the destroyed Raggs Kingdom. Teito is found eavesdropping and tries to attack his father's murderer but is quickly brought down by one of Ayanami's subordinates and sent to prison. Mikage comes to help him escape, only to find that Teito has managed to fight past the guards by himself. The two flee the building but are cornered on a balcony. Teito pretends to hold Mikage hostage, threatening to kill him if the guards pursue him, and thus makes his escape, though he is wounded by a Zaiphon blast that Ayanami directs at him. Three bishops in the nearby 7th District discover the injured Teito and take him to the 7th District church to recuperate. Because of the 7th District's law of sanctuary, as long as Teito stays in the church, the army cannot arrest him.