Sakura Sakurakouji witnesses a large group of people being mercilessly burned alive in blue flames as a boy watches with cruel eyes. Moved by her unwavering sense of justice, she returns to the scene the next day. However, neither she nor the police is able to find any bodies or evidence that could suggest such a crime had taken place.

At school, she meets new transfer student Rei Oogami, a charismatic boy that quickly wins over the class. Sakura recognizes him as the murderer and quickly learns that Rei is someone who exists outside the law: a "Code:Breaker." Despite him justifying his actions with the phrase "an eye for an eye, a tooth for a tooth, and evil for evil," Sakura is convinced that what Rei is doing is wrong and aims to stop him before anyone else gets hurt.