Code:Breaker follows Sakura Sakurakouji, a cheerful-looking girl whose delicate appearance hides a skilled martial artist and an unshakable sense of fairness. One day, while heading home, she sees people burning in blue flames on a bus and immediately calls the police, only to find that the crime has left no evidence behind. The mystery becomes even more unsettling the next day when Rei Oogami, a new transfer student, joins her class and turns out to be the same boy she saw commit murder in cold blood.
At school, Rei is kind, sweet, and quickly wins everyone over, making Sakura’s accusation sound impossible. Before long, she learns the truth: Rei is a Code Breaker, one of the "ones who do not exist," and he wields mysterious powers to carry out justice according to the principle of "an eye for an eye." Refusing to look away, Sakura stays close to him and tries to pull him back toward the right path before more people are hurt. As their uneasy connection deepens, Sakura’s belief in fairness is tested against Rei’s ruthless understanding of justice.