One night, Kazuki Muto jumps in to try to save what he thinks is a girl in distress from a monster and instead gets impaled through the heart. The girl, Tokiko, is actually an alchemic warrior with a Busou Renkin, name of Valkerie Skirt, with the mission to exterminate Homunculi. She implants the only other successful work of alchemy than the Homunculus, the Kakugane, to take the place of Kazuki's heart. The Kakugane resonates with his fighting spirit and forms a Busou Renkin (in his case a spear) so he can fight the Homunculus monsters who prey on humans. Kazuki joins with Tokiko to battle with the Homunculi and protect his friends and his sister Mahiro.