Shiki has a secret. Ever since the accident, he could see lines in every object. By passing a blade through these lines, he could easily cut apart anything. Troubled by this ability, young Shiki is given a pair of glasses by a lady he meets (Shiki calls her "Teacher") which hides the "lines of death" from his sight. Thanks to this, Shiki was able to live normally up until now.
However, circumstances change. A letter for Shiki arrives informing him that the head of the Tohno Household, his father, has died. By orders of the new head of the household, he must return at once to the Tohno house.
The story begins when Shiki, now a highschool student, returns to the Tohno Household. On his first day, he kills a woman in a fit of insanity. However, his 'victim', Arcueid, turns out to be an immortal, a vampire, and she enlists Shiki's aid in a conflict between opposing vampire factions.
From the start, the mutual attraction between the two is undeniable. However, dark secrets overshadow their burdgeoning relationship. Can Shiki overcome the various obstacles before him? Obstacles brought about by blood-thirsty vampires, by Arcueid's hidden past, by the unspeakable secrets of the Tohno Household, and by Shiki's own forgotten past. Finally, the greatest obstacle of all: Arcueid is still a vampire.