In Japan's not-too-distant future, crime has become so common that the government has legalised firearms for citizens to use in self-defence. To combat this new wave of wrongdoing, the Recently Armed Police of Tokyo was established in hopes of hunting down criminals with lethal force. Kyohei Tachibana is a gifted culinary student who dreams of saving up enough money to become a pastry chef in France. When four young mercenaries ask him to be their cook, he's forced into making a tough choice. As Jo, Meg, Sei, and Amy take on the bloodiest jobs in the chaotic city of Tokyo, Kyohei accepts an imminent descent into the world of crime—and he'll do a lot more than just cooking!

Amawa Hibiki is a young man just out of college, with an education to be an athletics teacher. He's been having a hard time finding a job since he graduated, so all his money has gone towards living expenses. When his landlady demands his first payment to live in her living establishment upfront, he heads to the local middle school to get hired as a teacher. However, the principal refuses to hire him without hesitation. She will not hire men as teachers and makes it clear that she hates all men, saying they put no love into their passions and work. Amawa does not give up and with the help of his landlady, he crossdresses as a woman without a second thought, and gets hired, so he can earn money and also prove the principal wrong. Now, he has to keep his real gender a secret, and avoid strange situations, including the affections of his students (from both genders).

The story takes place in Tokyo Butei High School, a special school where armed detectives—"Butei"—are trained to use weapons. Kinji Tooyama is a second-year-student who has a special ability, but he keeps it a secret to maintain an ordinary, peaceful life; however, when he gets caught in a bombing on the way to school, he encounters H. Aria Kanzaki, the most powerful S-Rank Butei student in Assault Studies.

Although cheerful and delicate, Sakura Sakurakouji is a skilled martial artist with a sense of fairness that never falters—no matter the situation. Upon witnessing people burning in blue flames while on a bus ride home, she calls the police to bring their murderer to justice only to find that no evidence remains. However, all her doubts about what she saw vanish when the next day, the new transfer student Rei Oogami joins her class; he is the very boy she watched commit murder in cold blood. Rei is kind, sweet, and quickly becomes popular, contradicting Sakura's accusations. Soon enough, she learns his true nature: a Code Breaker, or "one who does not exist." To Sakura's shock, Rei—armed with mysterious powers—seeks to exact justice according to the principle of "an eye for an eye." Determined to bring Rei to the right path, Sakura keeps close to him in the hopes of redeeming him from his ways before others are hurt. [Written by MAL Rewrite]