Humans live in the world of Assiah, demons in Gehenna. The two dimensions are not meant to interfere with each other, but demons still possess creatures in Assiah in spite of this. The humans who can fight these demons are known as exorcists. Rin Okumura is a boy who bears the curse of being Satan's illegitimate son. His foster father sacrificed himself to save him from demons. To avenge his foster father's death as well as to prove himself, Rin decides to follow the path of an exorcist and defeat his own father, Satan. To hone his raw skills, Rin enters True Cross Academy to train with other exorcist candidates.
Unlike his twin brother, Yukio, Rin Okumura never wished to know about their parents and the circumstances surrounding his own birth. Yet the master of time, Mephisto Pheles, gives Rin a key that transports him 40 years into the past when his late mother, Yuri Frederick Egin, was merely a child. With Mephisto's guidance, Rin leaps through the years of Yuri's childhood and her adolescence as an exorcist-in-training.
Early on, Yuri meets Shirou Fujimoto, Rin and Yukio's adoptive father. As Rin follows Yuri and Shirou's lives, he witnesses firsthand the initial appearances of Satan, his true father, and the horrors unfolding at the True Cross Order's special Section 13. Yuri's unique connection to Satan eventually leads Rin to the truth behind the most horrific event in exorcist history and the day he and Yukio were born—the Blue Night.