It's Too Late.

S1 E5: Kyou flees the school with Misuki, and the teachers manage to gain control of the school 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 himself. Aya and Izumi lose a battle against a student from class Z and Rex has to save them. Aya, Rex and Izumi think Kyou killed Todo.