As the result of a childhood injury, Shiki Tohno can see the lines of energy that bind all things together and by severing those lines he can destroy almost anything! Only a special pair of glasses that mute his extraordinary perceptions have kept him sane, but his attempts at living a “normal” life come to a shocking end when he is approached by a strange and dangerous woman. Now, Shiki is fighting both for his life and to unravel the secrets of his own past.
Shiki was seriously injured in an accident and he can't remember it.
Arcueid is on a mission to kill a serial vampire that is on a killing spree. Arc and Nero have to run away.
Shiki wakes up in Arcueid's room and discovers one of his friends is missing. Arcueid thinks Shiki has they eyes of death and is able to see death things. They also try to lure Nero and have have Shiki kill him.
Tohno goes back home but has a hard time explaining to Akiha where he has been. All his friends think he has a girlfriend.
Arc becomes upset because Tohno suspects her for some of the killings.
All the boys of 2-B are missing and have been turned into shishas. Tohno tells his friends that he will go to the amusement park with them this weekend. Arc starts working as a model.
Akiha finds out that Shiki is still sneaking out at night so she decides to follow him to the amusement park where he is to meet his friends. Arcueid joins the group at the park. Before everyone leaves to go home they find another victor of the vampire.
Shiki comes home from school and finds Akiha sucking the blood from one of the maids. Shiki also decides to study all the Tohno family death records and discovers that no one died of natural causes.
As Shiki is recovering at home he dreams of being a young boy and hearing a woman calling for him from beyond the trees. As he follows this voice he finds a trail of dead bodies. He then looks up only to find the voice of the woman calling him is lying impaled on a tree.
Arc tells Shiki that she will forgive him if he will go on a date with her. They end up at Shiki's school and while there his wound starts to bleed and he senses is attacker. Some zombies appear and attack but Arc fights them off.
Ciel tells Shiki that Arcueid was a pure moon princess that was tricked by the serpent Roa to drink human blood. As a result all she want to do is kill Roa over again. Shiki tells Arcueid that they can defeat Roa together. Akiha gives her Father's diary to Shiki so that Shiki can find out the truth about his past.
Shiki leaves to fight Roa and when Arc arrives he finds a mortally wounded Shiki but is still able to defeat Roa with the help of Ciel. Shiki tells Akiha that he finally has killed the real shiki and has been released of all his torment.