Following the events of Satsujin Kousatsu (Zen), Shiki Ryougi has been in a coma for two years due to a traffic accident. When she finally awakens, she has no memories of her past and is plagued by a profound loneliness. Even stranger, she notices dark lines encompassing the things around her, and if she touches them she can disassemble the object—something which completely terrifies her. Her friend, Mikiya Kokutou, enlists the help of Touko Aozaki, a mage who can help Shiki understand what her eyes—the "Mystic Eyes of Death Perception"—are truly capable of and how to use them properly.