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In the near future, due to an unusual rise in criminal activity, it has become legal to possess firearms in Japan so lawful citizens can protect themselves. At the same time, the government established the Recently Armed Police Taskforce, whose methods are exterminating criminals rather than arresting them.

The story opens with Kyohei Tachibana, a student at a culinary arts school with dreams of someday becoming a patissier, motorcycling down an inner city street and becoming caught up in a shoot-out between a mysterious silver-haired woman and a psycho gangster. Kyohei escapes unharmed and ends up working as a cook for Jo, Meg, Amy, and Sei in an effort to gather up enough money to travel to France. The girls, ranging in ages of eleven to nineteen, turn out to be pseudo-mercenary agents for a larger international group known as Bai Lan.

Chronos, an organization bent on world peace, rules one third of the world's economy. To maintain the balance of the world, Chronos is therefore essential, and there is a need for people to protect Chronos. Thirteen special elite assassins each possess unique orichalcum-forged weapons and are called the Chrono Numbers, assassins who work for Chronos. When the thirteenth Chronos Number (Train Heartnet), also known as the infamous Black Cat, meets a Sweeper (licensed bounty hunter) named Saya Minatsuki, Train's morals and values are changed from those of Chronos's to those of his own. Instead of killing his victims like he is ordered to, he merely uses Hades (his orihilcon gun) to stop them instead. This leads to tension between him and the Chronos Elders, the leaders of Chronos, and eventually culminates in Train's departure from the organization. Creed Diskenth, a Chronos assassin, resents the way that Saya changed Train's life, and murders her. Two years later, Train is an easygoing Sweeper, traveling with his partners Sven Vollfied and Eve, when Creed appears before Train once more. Creed, who Train believed dead, now holds awesome power, using ancient spells of Tao, something Chronos believed no longer existed after the War 20 years earlier. Creed, now with followers and power that rival anyone alive, including the numbers, vows to get Train to join him. Train must choose his friends and new life, or revenge, as Creed threatens to undermine Chronos and start his own World Revolution.