We open with Kuro attempting to wake Rin up. Rin however is very deeply asleep. Kuro solves this problem by jumping on Rin’s face. Yukio has apparently not returned from wherever he had disappeared to. Rin is understandably worried. Then he realizes that he is extremely late for class. He panics, and we go to the opening credits.
When Rin gets to school, he finds out that it’s been closed. He learns that the director of the school has been blamed for the hostage situation occurring, and has been arrested. He also discovers that the new Preceptor for the school is Yukio. Then he discovers that Yukio is also the Paladin of the order, and the person who put him in charge is their grandfather. Ernst is also apparently the Pope now. He has declared an all-out war against demons and even the student exorcists are expected to fight on the front lines.
Rin of course is more worried that Yukio got to be Paladin before him.
The next scenes are a montage of exorcists (including the students) attacking various kinds of demons. The energy from the demons is absorbed by the weapons and a large grimoire. As the fighting goes on, Shiemi and a few other of the kids start becoming unhappy with what they’re doing. In addition to honestly malevolent creatures, they are also killing demons that don’t actually cause harm.
In the next scene, Yukio is reporting to Ernst. Apparently the purge is going very well. He notes that some people are having a problem with the new method of demon hunting. Ernst states that sacrifices have to be made, and that Yukio should make sure that all of the other exorcists are with the program. Then Ernst notices Yukio seems to be unhappy about something, but Yukio states that nothing is wrong.
We next see Yukio walking down a hallway. He is remembering back to a previous conversation with Ernst. In the conversation, Ernst states that there may be a way to cure Rin of being a demon. Ernst tells Yukio that if they can destroy Gehenna, then Rin will no longer have the powers of a demon. Yukio is at first extremely skeptical that Gehenna can be destroyed, but Ernst reveals that he has a secret weapon. Ernst’s plan is to open a gate to Gehenna, and drop the bomb inside. (I am very strongly reminded of StarGate.) The catch is that the gate requires vast amounts of demonic energy, which is where the crusade against all demons comes in.
The next scene is back to Rin and the other students. They are camped for the night, and eating dinner. They seem extremely glum in contrast to Rin, who is as cheerful as ever. (Rin does not seem to be affected by most things that would upset or unnerve other people. And on the occasions where he is affected, it’s never for very long,) After some conversation, they are interrupted by a huge boar demon who is the protector of the forest. The boar is understandably unhappy with the invasion that has killed off most of his friends. He proceeds to tear the camp apart until he killed by Yukio.
This upsets Rin, and horrifies everyone else. An argument ensues about this, and ends with Yukio clawing Rin, and knocking him right off his feet. (Yes, literally clawing him, Yukio’s demonic heritage is obviously starting to show.) Yukio then makes a move to shoot Kuro, but the cat escapes. Yukio receives a call, and then orders one of the other exorcists to help him take Rin to Vatican headquarters.
When they get to headquarters, Yukio runs into Shura, who grabs Yukio by the arm and reveals that the dark blotches are all over his arm. Shura is extremely angry, because this means that Yukio’s demonic powers are now active, and that Yukio has been lying about the results of the tests he’s been taking. They argue, and Yukio states that it’s none of her business. He also states that when the war is over everyone will be “saved,” so it doesn’t matter. Shura questions him about that, but Yukio doesn’t answer.
In the next scene, Suguro is talking to the swordsmith who fixed Rin’s sword. He is consulting with her about the nature of the weapons they are using against the demons. She identifies the weapons as “blood sucking” weapons and tells him that this type of weapon should not be used. Suguro decides that he’s going to talk to Yukio and ask what the heck is going on, but Izumo points out that he won’t tell them anything. They decide to talk to one of the other teachers instead.
In the next scene, Rin wakes up in a cell. In the cell across from him is Mephisto. (Also present is Tiny Hamster Amaimon.) Mephisto provides exposition with an impromptu (and crudely drawn) series of pictures detailing his adventures. About five hundred years ago, Mephisto had been experimenting with artificial life. It turns out that Noihaus’ is in the teaching lineage of one of Mephisto’s former students. (That is to say, Noihaus is the student of a student of a student and so on of Mephisto.) Because of this connection between Mephisto and Noihaus, Mephisto has been arrested on suspicion of experimenting with artificial life. Mephisto however states that Noihaus (and by extension himself) have been framed by the same person. Then Mephisto turns into a dog and escapes. Shortly after that, Ernst turns up and introduces himself to Rin. It is not a happy meeting.
In the next scene, we discover that Rin is apparently going to be taken up to the roof of the True Cross Academy and executed. Rin’s friends are understandably horrified. Then the scene shifts to Rin, who is being escorted to some kind of x-frame in the middle of a pattern.
The kids and one of the instructors attempt to intervene, but they’re stopped by Arthur who is attempting to pull off a “none shall pass.” The scene shifts to Rin, who has been tied up to the x-frame. The ritual begins and the pattern begins to fill up with blood from all the gathered blood sucking weapons. Rin is also bleeding and screaming in pain. The scene shifts back to the kids. Suguro is demanding to know why Rin is being executed. Arthur states that it’s because he’s the son of Satan, which makes all of the students extremely unhappy. Arthur attacks the kids, but he is blocked by Shura. Shura tells the kids to go on ahead, which they do.
Yukio meanwhile, is extremely unhappy with what his grandfather is doing to poor Rin. Yukio demands an explanation. Ernst reveals that he is really the worst grandfather in the universe. His plan is to use Rin to open the gate, something that Rin was never intended to survive. Yukio is horrified, and then we go to the ending credits.
In the scene shortly after the credits, we see the kids entering the area where the ritual is taking place. The kids see a figure engulfed in flames, but it isn’t Rin. It is Yukio. Then the scene fades to black.