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.

August 1995: Mikiya first meets Shiki in a white kimono during a snowing day. Later on, at the high school freshmen ceremony, Mikiya sees Shiki in the crowd and chases after her, introducing himself to her. But Shiki hides a big secret: A wave of bizarre murders occur around many loose ends, and no suspects. there are still many questions: Who to believe? Who is the murderer? What is the secret of Shiki? and especially: Who is SHIKI?

In a post-war alternative timeline, Japan is divided into the North, controlled by the Union, and the South, controlled by the United States. A mysterious high tower rises within the borders of the Union. Three high school students promise to cross the border with a self-built airplane and unravel the secret of the tower.

March 1999: Mikiya Kokutou meets Shiki Ryougi again at the same place where he met her for the first time four years ago...

June 1998: After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. She is visited by Touko Aozaki, a wizard and proprietor of a studio called Garan no Dou. Shiki has lost not only the memory of her accident, but also any real sense that she's even alive. Strangely, enigmatic beings begin to attack her...

July 1998 - After a group of delinquents is found dead in their hangout place with all their limbs twisted and torn off, Aozaki Touko receives a request to find the murderer and asks Shiki for help. The main suspect is Asagami Fujino; a girl who was the boys' plaything until recently, who Shiki believes to be "one of her kind".

February 1999. Both ceremonies disappeared before Mikiya Kuroiri. And a continuous hunting murder case that recurs to match it. Three years ago, he called himself a murderer. Mikiya vowed to continue believing. Mikiya begins investigating the murder case to prove the innocence of the ceremony. Meanwhile, Mikiya reunited with a senior high school senior, Sakuji Shirazumi, triggered by a drug case.

Though Kevin has evidenced 23 personalities to his trusted psychiatrist, Dr. Fletcher, there remains one still submerged who is set to materialize and dominate all the others. Compelled to abduct three teenage girls led by the willful, observant Casey, Kevin reaches a war for survival among all of those contained within him — as well as everyone around him — as the walls between his compartments shatter apart.