In February 1999, a string of murders has Shiki Ryougi and Mikiya Kokutou on edge. These crimes share a disturbing resemblance to a similar set of homicides from 1995, when Shiki and Mikiya first met, and awaken a dark, murderous desire that has laid dormant within Shiki's soul ever since then.

January 1999: Apprentice mage Azaka Kokutou, Mikiya's younger sister, has been ordered by her mentor, Touko Aozaki, to investigate a certain incident in which fairies steal the memories of students at Azaka's school, Reien Academy. Azaka launches an investigation with the help of Shiki.

In 202X, Tathagata Killer, a mysterious military leader armed with extraterrestrial technology, stages a coup and becomes the new emperor of the world superpower of Asia. Sho Shishimaru, gifted with prophetic powers, may be the only one standing in the way of Killer’s take-over of the entire world. The future of humankind is at stake in this epic struggle, but in its midst, we learn about the mystical laws that rule the world around us.