Strange suicides shock the entire country, especially because all victims visited the same school. Weiss get assigned to the case, so Aya enters the school as teacher and Sena gets student. Sena soon finds a friend Nozomi Miyazawa. Together they talk about the things at the school. Sena soon gets in deeper and deeper. All students get a video with violence on it and students were taken out of class to a strange building. The next day Todo another student tries to kill him, but Sena stops him and has to pay for that.
Nozomi goes nuts, because he just had to kill his friend. Izumi talks to her, but immediately five killers show up and try to kill the girl. Nozomi is attacked not only physically, but also mentally when someone hacks into her computer and write murder all over her display. Nozomi can't take it anymore and jumps out the window right in front of Izumi's eyes
Izumi still can't believe that Nozomi killed herself. Kyou and Aya go to school again because the suicides still go on and they still have to stop them. Meanwhile Todo gets in trouble because he killed a student without an assignment. He also plans to kill Inagaki. Fot that he manipulates Izumi, so he goes and kills Inagaki. Aya and Kyou are too late, but learn some important information from Rex.
Aya and Rex are angry at Izumi, because he didn't fallow orders and killed Inagaki. Kyou on the other hand helps Izumi and tells him that he liked to kill Inagaki too, but didn't had time for it. Aya and Kyou go back to the Koua Acedemy. There Todo unites the students behind him and takes over the school. Todo gives order to kill Izumi and Misuki (Todo's girlfriend) to blow the cover fo Weiss. Kyou can't stand it and goes to save Izumi and blows his cover.
Kyou takes Misuki hostage and flees out of the school. The teachers manage to get the students back in to class and gain the control again. Todo finds secret documents about Inagaki. Inagaki was a cylon, a clone, the first prototype. When Kyou finds Todo in the secret room, Todo kills himslef. Aya and Izumi loose a battle against a student form class Z and Rex has to save them. Aya, Rex and Izumi think Kyou killed Todo.
Ken and Yoji get their own mission to handle things with the Z class. Things end with Yoji blowing up an entire building and a crazy woman, Yoji knows, crawling out of the destroyed building. Ken enters the control room steals all data and kills most members there. Aya and Izumi think about their lives and their membership to Weiss. Although Ken and Yoki doesn't come back in one piece they have to go to the school from now on too.
Yoji starts to work as teacher like Aya and Ken pretends to be a student. Yoji is jealous of Klaro because he flirts with all female colleges, especially with Tsujii-sensei. Aya and Ken find the secret place Todo learned the truth, but they are too late. All evidence is long gone. Omi thinks about telling the others about Persia.
Omi tries to tell the others about Persia, but he doesn't know hoe and so the others don't listen to him. Omi is hurt by that fact and takes a few days off. Back at school Ken is having trouble with the other students, because he is always together with Aya and Yoji, the two teachers. The three find new evidence, but they start to think that the connection of everything might not be the school after all.
The search for answers now goes outside the school, but strangely all answers they find were in the school. Omi is still missing and so Izumi goes for to search for him. Persia is watching the guys from Weiss now closer than before.
Weiß becomes the target of more and more enemies and the so Weiss is struggling to find more answers. Aya also get his personal trouble.
Sena find out the secret of his family. Meanwhile Weiß comescloser. to the solution of their problems.
Weiß finds out who Epitaph really is. The more information Weiß finds out about this organisation the more difficult their missions become.
Weiß takes on their last fight. They want to destroy Epitaph, even though she is prtected by her clones and the most dangerous people in the world: Rosenkreuz.