Teito Klein is a young student at the Barsburg Military Academy living with his best friend Mikage. They are getting ready for their final exams using their abilites, the Zaiphon. Teito stumbles upon a dark secret pertaining to his hidden past (which he is unable to remember) and attempts to escape from the Academy. Attempting to assassinate Ayanami, the man who killed his father, he is captured and sent to a cell. However, he escapes with the help of Mikage and manages to break free from the academy.

After Teito crashes, one of the men, Frau, carries him to the Church. Teito attempts to escape, only to be brought back into the church. The three men introduce themselves as Frau, Castor, and Labrador- all bishops of the Church, which lies in the 7th District of the Barsburg empire. Teito wonders about the condition of Mikage, who had helped him escape from the Academy. Teito enters the Library, wishing to know more about his murky past and his connection to the Raggs Kingdom. He decides to find out the truth about the Raggs Kingdom and his past. Meanwhile, back at the Academy, Mikage is questioned by Ayanami as to whether he helped Teito escape or not. When he refuses to answer, Ayanami gives him a choice: either to save his family, which he treasures, or to save Teito.

Teito decides to leave the Church and help Mikage. Teito stumbles upon an old man who tells Teito he can grant his wish. Teito then decides to run off by himself. Frau interrupts his thoughts, telling him that it might be his fate that he came to the Church. Frau and Teito fight using Zaiphon powers, but Frau is too strong and gains the upper hand. Castor realizes that Teito is a member of the Academy (as only those people have the ability to wield the Zaiphon). During the fight, Teito finally reveals his name. After waking up, Teito decides to go to the courtyard, where he sees the old man from before. Frau, realizes something is wrong. In the meantime, Mikage at the Academy is still unsure of which side to choose: either saving Teito or his family (namely his sister).

Teito talks with the old man, and tells him his wish to see Mikage. The old man places an odd symbol on Teito's neck while Teito has a vision of running toward Mikage. The flower that Labrador gave him from before stops him, and he realizes that the Bishops are there in front of him. Frau begins to attack the old man, who turns out to be a "Kor". The Bishops fight the man, and though Teito wants to help, Castor tells him he will only hurt the man's soul. Frau manages to release the Kor from the old man's soul and then get's rid of the symbol on Teito's neck. Teito asks Castor what a Kor is. Kor are creatures that tamper with men's desires- they grant the man's wish, but he or she is then put into a string of dark events in which the person is never satisfied with his or her wishes and eventually falls into darkness, becoming a host for the Kor. Back at the Academy, Mikage makes his final choice: he won't betray his best friend. An enraged Ayanami releases a surge of Zaiphon at Mikage.

The bishops wonder what Teito's wish was. Teito is still affected by the events from the previous episode and after offering to help out the sisters, wonders why everyone is so kind to him. Teito has a vision where he realizes that he is the heir to the Raggs Kingdom and The Eye of Mikhail. While walking to the gate of the Church, Teito is shocked to see Mikage walking towards him. Mikage decides to stay with Teito at the Church, and while they are talking, they are attacked by a Kor sent by Ayanami. Teito fights the Kor, but can not hurt it. Frau appears and cleanses the man's soul from the Kor. At night, Teito reveals to Mikage his connection with the Raggs Kingdom.

Teito and Mikage go to the church festival where even the bishops themselves open up shop. Unfortunately, bishop Frau is a bit too creative to work around the rule that forbids the eating of meat and the boys leave the festival when a young maiden appears at the front gate in her carriage. The girl seems to be very sick and bears the mark of a Kor, a powerful daemon. Mikage tries to save her by rushing her into the church to get help from the bishops. Unfortunately he does not get far before the Kor emerges from the girl and Mikage and Teito wind up fightng for their lives.In a dire situation, Teito displays a hidden power by accident which scared the Kor long enough for one of the bishops to rush in and safe the day.

Unbeknown to Teito, he and Mikage get to spend one last day together on the bazaar held at the church. This festival is meant for children of war victims and the two friends help a small boy who has the same sadness in his eyes as Teito once had. When the lost father of the boy appears to take his son home, everything will be alright.... or will it?

As Teito and Mikage talk, Labrador predicts that the “storm” will come very soon, and right now is the “calm”. Mikage suddenly feels something inside of himself awaken, and as one last favor...asks Teito to kill him. Mikage begins to scream in pain. As his last words, Mikage tells Teito that he loves him and that he’s always considered Teito to be just as important as his family. Ayanami possesses Mikage, releasing only one Kor wing. Teito and Ayanami fight, but Teito is injured and escapes with the help of one of Castor’s doll. Meanwhile, at the main Church, Castor senses that his doll has lost signal and Frau senses that a half Kor has entered the church. He goes off to find Teito. Teito in the meanwhile, has been found by Ayanami, and Teito begs him to give Mikage back. Ayanami puts a restraining collar on Teito's neck. Teito attempts to commit suicide, only falling unconscious. A guardian appears, and there is a flash of light as Teito’s eyes open, revealing his pupils to be blood red. Ayanami looks down in surprise as Teito asks “Who are you to hurt my master?”

Mikage, controlled by Ayanami, is still fighting Teito while Frau is on his way. Teito finally awakens with his eyes bloody-red and the Eye-of-Mikhail on his hands. The Collar on Teito's neck is close to bursting. Half out of control, Teito sends out multiple shots of Zaiphon damaging mass of the room. Ayanami uses a Binding-Zaiphon to strangle him and stop him, so he can't do much damage. Frau finally appears recognized by Ayanami as the God "Zehel", one of the Seven Ghosts. Frau cuts off the strangling Threads from Teito and tries to stop Ayanami. Ayanami and Frau have a little discussion. In a short period of time where the scythe is close to Mikage, Ayanami takes action and pushes the Scythe away. A short part of the Wing is cut off. Ayanami stops controlling Mikage, while Mikage's Wing starts to shatter. Feathers appear and Mikage is starts to vanish. Frau then takes Teito to his dorm. Moments appear, where Teito and Mikage befriended and some things what happened. Frau visits Teito, and Teito notices a cute pet which is crawling close to him, which turns out to be the reincarnation of Mikage. Frau tries to remove Teito's collar but ends up making pact with him meaning Frau has become Teito's master.

Teito decides to leave the church believing he should not cause anyone anymore trouble, on the way he meets Castor who asks him if he knows the shinigami Zehel. When Teito reveals he knows it was Frau, Castor puts him to sleep. As Castor gets ready to erase his memories, Frau interferes and says that if he is to erase his memory of seeing him as Zehel, then he will also forget Mikage's last smile. Frau's scythe goes out control and tries to attack an unconscious Teito, who awakens as the god Mikhail. Mikhail then uses illusions to try and threaten Castor and Frau but the two seem fine, Mikhail realising that they are the seven ghosts says that if they were normal humans then their minds would have drove them crazy. Castor tells Frau that the collar on Teito's neck has three commands: Bind, Sleep and pain. Frau puts the god to sleep with the sleep command. Teito regains concisousness and is taken to a place showing Mikage's last words.

Teito, now staying in the church, wonders what he can do to atone for Mikage's death. Castor advises him to take the Bishops Exam. Teito decides to take it, and Castor says he must pass the written exam first: memorize 7700 chapters from 77 volumes of Barsburg Bible in half a month. It took Frau three years to memorize it, but when Teito takes a look at one of the books, he realizes he has read them before. Teito reveals he remembers most of it. The second exam tests the person's ability to use Zaiphon techniques. When Teito doesn't progress with using a bascule, or staff, Castor gives Teito a Frau doll with incredible speed. After the doll acts like a pervert to the three sisters, Teito activates the staff and blows the doll up. After a talk with Labrador, Teito decides to learn and expose the truth of the world. While wandering in the hall, Teito sees a person looks like Mikage, but unfortunately is an examinee named Hakuren Oak. Hakuren sees the Bishops Exam Participating Mark on Teito's neck and declares Teito his rival.

In preparation for the priesthood exam, Teito is assigned a new room to live in. However, Teito discovers that Hakuren is his roommate, which only leads to more squabbling between the two. Later, Teito and Hakuren go to the practice hall, where numerous Kor are contained within a barrier of water. Hakuren shows everyone in the hall his ability with exterminating Kor, and Teito learns more about controlling a baculus. Meanwhile, Ayanami begins a dark and deadly scheme.

As a murder investigation is underway, Teito spends his time looking for more information regarding the Eye of Mikhail. He doesn't have much luck however, but he does realize that his powers are starting to awaken. Later, Teito goes to speak with Frau about the night of the murder, and overhears a revealing conversation between Frau and Castor. Not long after, Teito confronts Frau about what he heard, and in the end Frau encourages Teito to prepare himself for the conflicting future. Meanwhile, a familiar enemy manages to discreetly enter the church grounds.

Castor assists Teito with his training by creating several more puppets for him to race against, and later gives him a new baculus to practice with. Upon the end of the training, Hakuren makes his presence known, then he and Teito begin the walk back to their dorm room. However, they are soon attacked by a new enemy, and Frau appears to save them from certain death. Frau manages to fend off the enemy for the time being, but the attack raises a great sense of unease amongst the bishops.

An unexpected messenger comes before Teito, and his cruel words leave Teito with conflicting thoughts. Not knowing what to believe in anymore, Castor and Labrador help Teito by bringing him to a special room capable of showing a person's true feelings. Meanwhile, Frau confronts an enemy; and, in the process of trying to save someone, falls for a sinister trap.

Teito receives some surprising information from Castor concerning Father, and how his actions might have been the precursor to the fate of the Raggs Kingdom. Teito decides that he will have to search for the truth, but first he must pass the priesthood exam. Labrador learns something shocking about Frau's situation, and Teito goes with Razette to the Dungeon of Light, where Frau is being held.

Teito and Hakuren go to search for evidence proving Frau's innocence, but come across Bastien instead. After hearing tales of Frau's childhood, Bastien bids farewell and leaves them. Not long after, Teito and Hakuren notice their Baculus' have been tainted, which they realize could have only been done by one man. With the horrifying truth now known to them, Teito and Hakuren go to confront the one responsible, leading to a fight and discovery of dark intentions.

After Teitos knocked out, Hakuren continues to fight Bastian. Meanwhile Castor and Labrador decide to take action against the intruder. The inturder is Kuroyuri and Haruse from the Black Hawks. Hakuren was captured by a Wars and Teito is imprisoned in some kind of ball where a lot of Wars reside. Teito and the Eye of Mikhail begin to fight over control and while they do that some Wars enter Teitos body. Frau finally shows up and saves Teito and Hakuren. Kuroyuri goes to kill Frau, but ends up killing one of Castor's dolls instead. While he does that Haruse fight Labrador. Then he and Castor begin to fight.

While participants in the examn of the church gather, the battle between the soldiers of the army and the protectors of the church continues. Bastian-sama gets a proper funeral to keep the truth under wraps and make life continue as normal. Meanwhile, Hakuren gets his up close and personal encounter with the Eye of Mikhail while he is taking care of Teito. After Teito wakes up, the darkness in his heart awakens the darkness that escaped into the Eye of Mikhail and Hakuren barely manages to grab Teito as the darkness engulves them both...

After being captured by Ayanami, Teito and Hakuren escape the military air ship and get support from Frau. After an intense battle the Eye of Mikhail attempts to save Teitos life by seperating itself from Teito and taking the Wars with it. After seperation the Eye unleashes its full power to destroy the enemies threatening Teito, making it rain fire upon the enemy air ships. Frau decided to save Teito and leave the Eye of Mikhail to fall in enemy hands. After cheering Teito up for losing the Eye of Mikhail, the other bishops give Frau a plant. Because bishop Bastian fell into the darkness, he was not reborn as a human, instead he was reborn as a tree. Frau planted the tree in the garden of the church so Bastian would be with them for many years to come. Teito finally recognises Hakuren as his friend and prepares for the bishop examn. On their way to the examn Teito accidentally steps on a key token that one of the bishops dropped and broke it. Unfortunatly for Teito, that same bishop, Lance, is their head examiner...

The military found out about the Eye of Mikhail and its master, Teito, and decide to search for him. Teito finds out that his Zaiphon seems to have been drained since the leaving of the Eye of Mikhail. One of his friends gives Teito some of his energy to allow him to be able to continue. After the examn starts, all the aspirant bishops enter the first hall. This chamber uses the fear in peoples hearts to hold them down, after Teito gathers his resolve he manages to walk out as one of the first. The next challenge is to answer questions in several rooms using their Zaiphon while trying to stay alive. Halfway through the examn, Teito decides to help the old men to cross the rope bridge. Finally they reach the last challenge: the challenge states that only one of them can pass through the door of Victor and the other has to use the door of the Defeated. After fighting each other, the winner has to write his name on the wall before passing through the door of the Victor. After arguing about it, they both run off through the door of the Defeated. After passing, a voice inquires why they choose this door and Hakuren replies: "Nobody has been defeated and nobody has won" at which point Teito says: "I'm just here to be with my friend". Bishop Lance appears and tells them that their selfless solution made them pass.

After passing the first examn, Teito and Hakuren get to see the progress of others and how some fumble at the last challenge when their greedy nature makes them fail. Teito and Hakuren learn that the old guys they helped before were in fact Former Assistant Archbishops who tagged along to asses the progress of the participants. Meanwhile, the protectors of the church prepare for a dark threat as the military advances towards the church. Teito and Hakuren go to Lazet, the mermaid, as the Former Assistant Archbishops suggested and she takes them to a inner sanctuary where Teito gets to see his father and Father, the priest who raised him. He got told to never forget who he is, the Prince of Raggs Kingdom. Afterwards, they hurry back to the courtyard where bishop Lance is impatiently waiting for them. The second part of the examn is a challenge to face their inner daemons inside a room. They pass when they come out the other door. Hakuren starts of by defeating a gigantic Wars and Teito faces his biggest enemy: Ayanami in the flesh...

The second examn resumes for the remaining trainees and comes in the worst form imaginable: the physical realisation of their deepest fears. When someone fails to overcome their fears, they fall through the bridge and fail. Teito gets to face his biggest enemy, Ayanami in the flesh. After charging blindly at Ayanami, Teito gets to see visions of the hurt and pain he caused Mikage and his family. Meanwhile, Hakuren finds his hated father on the ground with an unknown person in a black cape and weapon standing over him. Hakuren sees a vision of his father telling him he is no longer his son if he joins the church. The grim reaper tells Hakuren they should finish his father's pathetic, heartless life. The constant talking about Hakuren finally gets to Teito who is starting to blame himself for everything he has done to his best friend. When Ayanami charges at him, he is petrified and unable to move to dodge the attack and gets impaled by Ayanami's sword. Finally, the last trainees that haven't failed yet find the strength to face their fears. Hakuren saves his father and forgives him. Teito on the other hand is starting to go in shock. Some of the examinators worry for his life and urge bishop Lance to terminate the examn. It is then when Teito figures out that his real enemy is not Ayanami but himself, the part of him that is blaming himself for getting Mikage killed. When Teito is ready and attempts to leave the second examination, the rest of the church gets invaded by the imperial army. And when Teito opens the door to exit the examination room, he finds himself in a dark, underground corridor instead of the exit. After a few seconds someone walks from the darkness towards Teito and this time, it is the real Ayanami who is standing in front of him...

Ayanami appears in front of Teito and Teito wonders if Ayanami is just an illusion like before. Ayanami mocks Teito for still relying on the Eye of Mikhail when it is not even there anymore. Ayanami uses his Zaiphon to bring Teito and himself to the center of the earth, where he threatens "it is the first and last world you shall ever see". Teito attacks Ayanami, who mocks him for being weak. Ayanami tells Teito to attack him for real, and Teito asks why he is here. In the hall, Frau is still waiting for Teito to exit the examination room and Hakuren runs up to him to tell him that imperial forces have stormed the church. Suddenly, Kuroyuri appears saying sie wanted to kill the gardener (Labrador) who killed Haruse. Bishop Lance gets into a fight with one of Ayanami's men. Ayanami asks Teito if his memories of traveling with Fea Kreuz have returned yet. Castor captures the man who was the spy in the church and asks why he became a puppet of the military. Labrador erases the memory of the spy, so he may start anew when one of Ayanami's men kills him. Ayanami's men attack Castor and Labrador and Labrador is thrown aback. Bishop Lance defeats the man who was attacking him. Kuroyuri throws dark energy at Frau and tells him to show his true form as Zehel. Ayanami, meanwhile, is trying to access Teito's memories but Fea Kreuz (Vetrag) is stopping him. Ayanami's arm gets torn off and Teito realizes that Father was one of the Seven Ghosts. Ayanami's arm regenerates and Teito knows he has to live for those who died for him. He throws another attack at Ayanami that gets deflected and Ayanami tells him that he hasn't changed at all. Frau keeps using his scythe to cut away at the darkness that Kuroyuri is emitting. It seems Kuroyuri is falling apart from the same thing that killed Haruse. However, the more Frau attacks, the darker Kuroyuri becomes. Teito and Ayanami continue fighting, and Mikage gets hit by one of the attacks. Teito runs to catch the falling Mikage and realizes he has to remember what he is fighting for. Kuroyuri is pushed back by Frau's light, which he calls love. Frau tells Kuroyuri hir justice is flawed and the black flowers Kuroyuri was holding fade away. Ayanami tells Teito to search his memories for the location of Pandora's Box, or the hostages in the church will die until Teito remembers.

Teito uses the power of the Eye of Mikhail to summon Frau, Castor, Labrador, Lance, and the Black Hawks. He then sends them, himself, and Ayamani to a white place where they're surrounded by giant figures of the Seven Ghosts. Both groups start to battle each other in earnst. They become locked together in battle, until Ayamani splits the bonds. Then he and the rest of the Black Hawks disappear through a portal Kuroyuri summoned. Frau and the others disapear too, leaving Teito alone with Mikage in human form. They talk then Teito also leaves. Frau, Labrador, and Castor are all waiting for him as he exits the Bridge of Trials. They tell him that he passed the exam and is now an apprentence Bishop, with his mentor being Frau. They then tell him that he and Frau are gong to escape through a secret passage built for the Pope in case of emergency. While they run towards the secret exit, Teito runs into Hakuren. They talk briefly, then Teito continues to run with the others. Before they leave Teito declares his intentions of what he wants to do from now on. Everyone approves and he bids them farwell. Frau and Teito get on a Hawkzile and with Labrador's flower guide, make their escape.