The film begins at a warehouse party with loud music that is attended solely by gangsters. At 2:30 AM, Killer Bean is at a nearby hotel trying to sleep, and makes a phone call asking them to turn down the music. The gangsters refuse, and Killer Bean confronts them. After the gangsters fire a shot at Killer Bean and miss, Killer Bean ends up killing every one of the gangsters. The last bean killed is revealed to be the nephew of Cappuccino, a mob boss.
The police, led by Detective Cromwell, investigate the warehouse shootings. The warehouse is known to be owned by Cappuccino. As the police investigate, Vagan, a lieutenant of Cappuccino, arrives at the warehouse. After discovering the massacre, Vagan, who runs guns for Cappuccino, quickly informs his boss what has happened and that Cappuccino is Killer Bean's next target. Due to Killer Bean's skill, Vagan suggests hiring mercenary soldiers to kill him.
Killer Bean receives an encrypted call from his boss warning him that he is being reckless and that the attack on the warehouse should have never happened, and that only the "target" should be killed. Killer Bean ensures his boss that the mission will succeed. Killer Bean goes to another of Cappuccino's warehouses but instead finds Vagan there, who attempts to kill him. The fight between Vagan and Killer Bean ends as a draw. Vagan leaves a note to Killer Bean which reads, "Shadow Bean, you are too late".
Killer Bean later goes to a bar across the street where Detective Cromwell finds him. Cromwell suggests they work together to bring Cappuccino down, but Killer Bean refuses his help. Later, Cromwell finds the note referencing the "Shadow Beans". After a call to police intelligence, Cromwell discovers that the Shadow Beans were a private organization that carried out secret government operations, but disbanded years ago.
Killer Bean locates a third warehouse, evidently attempting to find Cappuccino there. After killing the gangsters there, Killer Bean is confronted by mercenaries hired by Vagan. The mercenaries fail, but afterwards Vagan is able to capture Killer Bean. Cappuccino interrogates Killer Bean asking him why he wants to kill him, but receives no answers. Killer Bean escapes, and then reveals that he is not after Cappuccino, but rather after Vagan. Cappuccino is then shot by Vagan. Killer Bean explains that he has been sent to kill Vagan, a former Shadow Bean whose code name is Dark Bean. Dark Bean had betrayed the Shadow Agency and had stolen their secret database. Dark Bean then explains that the Shadow Agency had degenerated from an honorable agency into simply guns for hire, and that he was ordered to supply weapons to criminals. Dark Bean claims to have left the Shadow Agency and run guns for Cappuccino so that he could be knowledgeable of all weapon transfers, and thus could fight crime. Killer Bean doesn't believe him, and kills Dark Bean as he attempts to shoot Killer Bean first.
Detective Cromwell witnesses the entire fight, and orders the entire police department to capture Killer Bean. Killer Bean gives up, assuming that only the police can protect him from the Shadow Agency, and presumably because he would have to kill police officers. Meanwhile, the Shadow Agency has dispatched another Shadow Bean named Jet Bean to kill Killer Bean. Jet Bean, an assassin from the east, is one of the Shadow Agency's top Shadow Beans.
Killer Bean is taken to prison, but Jet Bean manages to kill every police officer and find him in his cell. Killer Bean explains to Jet Bean that the Shadow Agency has gone criminal, but Jet Bean doesn't believe him. In the last fight scene, Killer Bean kills Jet Bean with much effort. Killer Bean then contacts the Shadow Agency on Jet Bean's cell phone, and they suggest Killer Bean come in to "talk things over". Killer Bean says he will come in, but it won't be for talk. The film ends with Killer Bean finding a cache of police weapons, and driving off to confront the Shadow Agency.