Yuuji Sakai, a high school student who expected his very normal life to last forever, is dead. While on his way home one day he witnesses a shocking view: the world suddenly freezes, people are engulfed by blue flames and a monster resembling a large doll seems to swallow them. Just as the monster prepares to consume Yuuji, a sword-wielding girl in black attire with flaming red eyes and hair that burns like embers saves him. The girl calls herself a "Flame Haze" who hunts the Tomogara (formally "Guze no Tomogara", or Crimson Denizens in English), creatures from another world. When Yuuji notices a blue flame in his chest, the Flame Haze tells him that the "real" Yuuji died some time ago, and that he is a "Torch", a temporary replacement for erased humans. Torches take on the forms of those erased persons, but before long, they will vanish from the memories of the living. Unfazed by his apparent death, Yuuji befriends the strange girl and names her "Shana". Expecting Yuuji to slowly fade away like all other Torches do, Shana is surprised to find that Yuuji is not a normal Torch, but instead a special kind called a "Mistes": he has a "hougu" inside him, and an extremely powerful and valuable one at that. Shana resolves to protect Yuuji from the Tomogara, who would use the hougu to disrupt the balance of the world, and Yuuji decides to join Shana in her fight.

Shana's fight is the long-standing struggle between Flame Hazes and Tomogara. The Tomogara are beings from the Crimson Realm and steal Power of Existence, the energy that forms the basis of the world, from the living people and utilize it for their own selfish ambitions. Flame Hazes are the mortal enemies of Tomogara, and attempt to retain balance. Thus, the Flame Hazes create Torches in the image of the dead in order to relieve the strain on reality resulting from the actions of the Tomogara.