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 who frequently has frightening dreams. The night before the graduation exam, Teito and his only friend, Mikage, vow they will never abandon each other. The next day, Teito overhears 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: his father, the king of the destroyed Raggs Kingdom. Teito is caught eavesdropping and tries to attack Ayanami but is quickly brought down by one of his 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, then 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 a nearby church to recuperate, where he is protected because of the 7th District's law of sanctuary.
In due time, it is discovered that Teito carries the Eye of Mikhail, a powerful talisman for which his home country was destroyed. This fact, as well as a fateful reunion, catapults Teito into a quest for revenge against the Barsburg Empire and for knowledge about his past. At the same time, his status as the bearer of the Eye of Mikhail throws him into the long-standing conflict between the evil Verloren and his enemies, the 07 Ghosts.