After Detective Shunsaku Aoshima is promoted to section chief he has the daunting task of dealing with eight cases at the same time, which includes a murder case, bomb threat, and a bus hijacking. Complications also arise between Detective Aoshima and his juniors.

Aoshima, a police detective working in the Bayside Precinct, is continually frustrated by the hierarchy and red tape that plague the system. His friend Muroi is climbing the ladder of the police bureaucracy. Muroi has made a pact with Aoshima that while Aoshima looks after the streets, Muroi would make life easier for the cops on the beat. One day in Bayside, a series of events turns the small station upside down.

The movie takes place again in the fictional Wangan Station of the Tokyo Metropolitan Police Department the once empty space within Wangan's jurisdiction has become a popular tourist attraction. When a string of murders of company execs begins taking place, Aoshima jumps at the opportunity to pursue something other than his current case, which he finds less than inspiring. However the powers that be have other ideas, and Wangan again plays host to a special investigation team from headquarters. Aoshima's friend Superintendent Shinji Muroi, assigned by headquarters to assist Okita, is again powerless to help the local officers as decisions are made by the higher ups.

Set 2 years after prior film "Bayside Shakedown 3: Set the Guys Loose," a major case occurs that has the potential to take down the entire police organization. For the next 3 days, Shunsaku Aoshima and his colleagues struggle to unravel the case...