The story begins when Kazuki Muto, a high school student, is killed one night while saving a mysterious girl from a monster, only to wake up in his school dorm believing it was all a dream; however, he soon discovers that dream wasn't a dream at all when a giant serpentine monster attacks him and his sister. The girl he saved, Tokiko Tsumura, reveals that the creature is a homunculus. When he was rescuing her, it attacked and killed him; but, feeling guilty for him, she restored him by inserting a Kakugane medallion in his chest, functioning as a new heart. Tokiko says that the Kakugane is an alchemical device that, when triggered, takes on a specific shape dependent on the Kakugane's owner.