In the world of Black Cat, Chronos, an organization bent on world peace, rules one third of the world's economy through underground control of almost every kind of business. To maintain the balance of the world, Chronos is essential, and there is the need for people to protect Chronos. There are special elite assassins with Orichalcum-made weapons called the Chrono Numbers who work for Chronos. When the thirteenth Chrono Number Train Heartnet, also known as Black Cat, meets a Sweeper named Saya Minatsuki, she opens his eyes and helps him see that he has choices as whether to kill his victims or not. He leaves Chronos but Creed Diskenth resents the way that Saya changes the elite assassin's life, and murders her. Six months later, Train is a Sweeper and travelling with his partners Sven Vollfied and Eve as the story follows their adventures of catching bounties and protecting/relying on one another.