The main character Tohno Shiki, was involved in a major accident in his childhood. He was so severely injured that people thought he was dead, but he miraculously survived. However, due to that incident, Shiki is sent away from the Tohno household and is entrusted into the care of a distant relative`s family.

There was a secret to Shiki. Ever since the accident -- lines at which things break easily could be seen. If a blade could be passed through the lines, anything could easily be severed.

Troubled with this ability, young Shiki is given a pair of glasses by a lady he meets (Shiki calls her "Teacher"), which stops the "lines of death" from being seen. Thanks to that, Shiki was able to live normally up until now. And he was planning to live normally from now on.

But then, a letter arrives for Shiki. The head of the Tohno Household - his father`s household - has died. By orders of the new head of the household, he must return at once to the Tohno house.

This story begins when Shiki, now a High School Student, returns to the Tohno Household.