From a bus window, martial artist Sakura Sakurakouji watches a boy stand unharmed over people burning in blue flame, but the next day there are no bodies and no sign of a crime. The same boy turns up in her class as a transfer student, Rei Ougami, who reveals himself as the sixth Code:Breaker, an assassin working for a secret government organization and answering evil with his blue fire. Sakura refuses to accept his kill-for-justice creed and attaches herself to him, set on changing how he works.