The artificial Gehenna Gate has completely opened, throwing the material world of Assiah into utter chaos as many humans have now begun to see demons. Amid everything, Yukio leaves the Knights of the True Cross and heads for the Illuminati. Rin decides that he must learn the secret of their birth. He embarks on a journey 40 years into the past with Mephisto's guidance. Rin witnesses the fated meeting between two individuals – an orphan who lives in an abandoned factory named Yuri, and a test subject from Section 13 named Shiro.

Shiro believes that an exorcist's duty is to destroy demons, while Yuri believes that an exorcist's duty is to help people, and advocates for building friendly relationships with demons. Shiro, irritated by Yuri's attitude, harshly confronts her. Time passes, and the two pass their Exorcist Certification Exams. Shiro finally achieves his dream of leaving the Asylum and begins living alone and indulging in his freedom. Yuri watches on in concern, but another mission puts the two at odds once more...