When things go bad in Beantown, top assassin Killer Bean is called to clean-up the mess. Detective Cromwell finds himself in the middle between Killer Bean and mob boss Cappuccino.

Taking place directly after the events of Killer Bean Forever, Killer Bean sets off on his quest to destroy the shadow agency.

Killer Bean has been imprisoned. After the blue beans have asked many questions with some punching, he introduces himself as being The Killer Bean. The interrogator gets scared when he discovers who he has been punching and attempts to run away, but a guard bean shoots him. The beans continue the interrogation with another bigger, stronger bean as the interrogator. After a few more kicks and questions, Killer Bean manages to take guns from his two guards' hands and kills every bean in the room in this epic first installment

During a loud party, a bean called Killer Bean breaks in, and begins to attack all the beans in the building.