The largest garbage strike in San Francisco history has just begun. Trash is piling up everywhere, and the sanitation union's boss, Jimmy Cusack, is promising a prolonged work stoppage. It's a nightmare scenario for Monk, and it's only made worse when Jimmy Cusack is found dead in his office of an apparent suicide. Suspecting foul play, the sanitation union suspends all negotiations with the city, and hires Monk to look into Cusack's death. If Monk agrees with the police that Cusack's death was a suicide, the union promises to return to the bargaining table.
Monk and Natalie head to Cusack's office to inspect the crime scene. Cusack was found dead from a gunshot wound to the head, holding a gun in his right hand. Monk desperately wants to rule the death a suicide, but clues at the crime scene seem to indicate otherwise. Nevertheless, Monk, eager to end the garbage strike, lies and tells reporters that Jimmy Cusack died by his own hand.
At Natalie's insistence, Monk comes clean and tells Captain Stottlemeyer that Jimmy Cusack was probably murdered. The Captain begins a full-on murder investigation, and the garbage strike continues. After some investigating, Monk concludes that the mayor of San Francisco was in Jimmy Cusack's office the night he died. Monk makes the mayor the prime suspect, and when this bit of news leaks to the public, union tempers are further inflamed. Unfortunately, when Monk digs further into the case, he realizes he made a mistake. The mayor is innocent, and, for the first time, Monk is wrong!
The disorder and smell from the mounting piles of garbage are affecting Monk's crime-solving abilities. Next, Monk comes up with an even crazier theory involving rock star Alice Cooper as the killer! Tired of being embarrassed by Monk's false theories, Captain Stottlemeyer takes Monk to a "clean room," where computer chips are fabricated. Protected from the smell of garbage, Monk is finally able to think clearly, and he quickly solves the case.
Here's what happened: Jimmy Cusack was killed by a union accountant, Ron Neely, whom Monk met at the original crime scene. Neely was skimming money from the union's pension fund, and he concocted a plan to kill off Cusack, make the death appear to be a suicide, and blame Cusack for the stolen money. Neely's big mistake was this: when he killed Cusack, he put the gun in Cusack's right hand. But Cusack was left-handed. Neely tried to cover his mistake, but he couldn't fool Monk! With the case solved and Neely in custody, the sanitation workers eventually return to their jobs, and the city of San Francisco is restored to cleanliness, ending one of the worst crises Monk has ever had to endure.