The story starts following an incident: a young girl jumps from the top of a building. The image provokes a certain dread, as the girl appears to have been a corpse even before she jumped. The case is dismissed, yet more and more of these suicides occur, and all from the same building. Thus began the rumour, that a ghost inhabited the rooftop of the building.

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?

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".

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.

Yuru, a young hunter, lives in a small village deep in the mountains, hunting wild game and leading a humble life with Asa, his younger twin sister. Their peaceful lives are torn apart when a dragon’s roar echoes across the sky. What secrets lurk within their village? What fate awaits them?

A side story of the original Kara no Kyōkai - the Garden of sinners movie series divided into 2 parts. In the first part, Shizune Seo, who finds her life too predictable due to her precognition, and Mitsuru‎ Kamekura, who uses his precognition to be a professional bomber, meet Mikiya and Shiki, respectively, and their futures begin to change. In the second part, 10 years after the original series, Shiki and Mikiya's daughter, Mana Ryōgi, spends a day with Mitsuru.

Mikiya Kokutou gives Shiki Ryougi a cat to watch, as he will be away for a little while. Though Shiki protests, he leaves the cat anyway, and Shiki is stuck trying to understand her new feline companion. But as luck would have it, the cat seems to have taken a liking to Mikiya and misses him. Later in another part of the city, Ririsu Miyazuki visits the place where her dear friend committed suicide. She intends to end her life as well, but she meets Fujino Asagami, a blind classmate with a traumatic past. Though the two girls don't have much in common, Asagami reminds Miyazuki of her lost friend and helps her understand her pain. Two months later, Mikiya elects to celebrate New Year's with Shiki instead of his family, which makes his sister Azaka very upset, leading to her spending the holiday with her school friends. As the snow begins to fall, Mikiya reflects on what he wishes for most of all: that Shiki's life be filled with happiness.