Having lost her family in a fire and with nowhere left to go, Yuri meets Shiro, who is on the run from Section 13. Shiro is brought back by the exorcists pursuing him, and he makes a request of Mephisto. Meanwhile, Yuri is taken to the Asylum, a school for exorcists-in-training, due to her ability to see demons. As he watches the two grow up, Rin witnesses the true nature of the Asylum and Section 13.

Nine years have passed. During that time, Shiro, Yuri, Rick and the others gained experience and grew up. Meanwhile, in Section 13, Elixir experiments continued. Although Amaimon successfully possesses a new body, Lucifer is still unable to find a suitable body, and in his suffering, his attachment to material things grows stronger. However, in the midst of this all, a being that is "the universe itself" incarnates in a certain test subject.