Riding the bus one day, Sakura Sakurakoji looks out the window to see people being burned alive with a blue fire as a boy her age remains unharmed and stands over the people. When she goes back to the site the next day, there are no corpses or evidence of any kind of murder, just a small fire. When Sakura goes to class, she discovers the new transfer student is the same boy she saw the day before. Sakura soon learns that he is Rei Ogami, the sixth "Code: Breaker," a special type of assassin with a strange ability and a member of a secret organization that serves the government.