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.

Yuri heads to Satan, who has holed himself up in Section 13. Satan accepts Yuri and chooses to live with her. To live together, he decides to abandon Section 13, informing his followers of his withdrawal. As Yuri prepares for their escape, she reunites with Jenny, who is working in Section 13. Upon learning about Satan and Yuri's plan to escape, Jenny plots to free the test subject children at the facility, but...