Tsukihime's plot follows the perspective of Shiki Tohno (遠野 志貴, Tōno Shiki), a second year high school student of Misaki Town, who suffered a life-threatening injury when he was young. When he regained consciousness, Shiki was able to see "death lines", lines by which things will eventually break when they die. This includes the death of inanimate objects as well as living beings and undead beings. Because of his Mystic Eyes of Death Perception making him see death lines Shiki has immense headaches as his mind cannot cope with the sight of death. Soon after he is given a pair of glasses from Aoko Aozaki that blocks the sight of these lines. The game then advances to Shiki's second year of high school. After his injury, he was banished to a branch family of the Tohno household. After eight years he is called back home by his younger sister, Akiha Tohno (遠野 秋葉, Tōno Akiha), when she assumed the responsibility as the family's head. After moving back Shiki has trouble adjusting to the old-fashioned lifestyle his sister lives by.
As the story progresses the plot diverges depending upon the choices the character makes. Shiki must use his powers to confront supernatural beings such as vampires, that are known as True Ancestor (真祖, Shinso) and Dead Apostles (死徒, Shito). The two plot routes that follow Shiki with Arcueid or Ciel are the Near Side of The Moon routes while the three routes that follow Shiki with Akiha, Hisui or Kohaku are the Far Side of The Moon routes.