Sakura Sakurakouji witnesses a large group of people being mercilessly burned alive in blue flames while a boy watches with cruel eyes. Driven by her unwavering sense of justice, she returns to the scene the following day. However, neither she nor the police can find any bodies or evidence suggesting such a crime occurred. At school, she meets Rei Oogami, a new transfer student and charismatic boy who quickly wins over the class. Sakura recognizes him as the murderer and soon learns that Rei is someone who exists outside the law: a "Code:Breaker." Despite his justification of "an eye for an eye, a tooth for a tooth, and evil for evil," Sakura is convinced that Rei's actions are wrong and aims to stop him before anyone else gets hurt.