Yuji has just started a new semester of high school and everything seems to be normal. That all changes one day when he goes out shopping after school. The entire world around him freezes except for two monsters that begin to devour the frozen people. Upon seeing him move they call him a "Mystes" and try to kill him.

Then a mysterious girl with hot eyes and long flaming hair comes to his rescue. She brings back all the people that were devoured and unfreezes the world. According to her she didn't bring them back, but created temporary replacements. She also says that Yuji is an extremely rare form of these replacements, or "Torches" known as a "Mystes" with a treasure inside. Thanks to this, more monsters will come after him, and she will protect him at all costs.

Set in the 16th century in Europe, this is a prequel story of Shakugan no Shana. In the world where the seals didn’t exist, the Great War burst between the Flame Hazes and the Crimson Denizens. The story centers around Mathilde Saint-Omer, the former “Flame-Haired Burning-Eyed Hunter” and reveals details that haven’t been explained in Shakugan no Shana.