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Based on a novel by Nasu Kinoko, writer for TYPE-MOON. Kara no Kyoukai plays in a parallel universe to that of Tsukihime.

After spending two years in a coma caused by a traffic accident, Shiki Ryougi awakens with amnesia. One day, Shiki is visited by Touko Aozaki, a wizard and proprietor of a studio called "Garan no Dou.

Mikiya Kokutou meets a girl who has a mysterious gaze, and falls in love with her. That April, at his high school entrance ceremony, Mikiya is reunited with the girl.

In the city where Shiki lives, something triggers a spate of mysterious schoolgirl suicides. The connection between the girls who leapt to their deaths is unclear, although all of them have jumped from the Fujou Building, a skyscraper scheduled to be demolished.

One night, Mikiya helps a girl who is lying doubled over with stomach pains. Around that time, a number of dismembered bodies are found throughout the city.

Shiki meets a boy named Tomoe Enjou, a runaway who claims to be a murderer. Shiki allows Tomoe to use her apartment as his hideout.

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 who can see fairies.