When Monk and Natalie arrive at an electronics store to meet Captain Stottlemeyer and Lieutenant Disher, they come across a disturbing crime scene. There's no body or murder; it's just a simple robbery. But the items stolen from the store are all bomb components - the exact ingredients used to build the bomb that killed Trudy. And on the crowbar left behind, the police find another intriguing clue: the fingerprints of a six-fingered man. Monk is rattled as he appears closer than ever to solving his wife's murder.
For the first time in years, Monk has a lead in Trudy's murder case. The burglar left behind a cryptic note, and Monk and Natalie devote themselves to trying to crack the code. They realize that the words on the piece of paper “To force heaven mars shall have a new angel" involve something happening at 11 o'clock that very night, but Monk is so distracted by a nightmare he had about Trudy that he can't focus on anything besides some orange juice missing from his refrigerator. Suddenly, Monk has a breakthrough, but he doesn't mention it to Natalie. Instead, he waits until she leaves, then grabs the gun out of his closet and hops on a bus.
He arrives at a sculpture garden located at 247 Marshall Avenue, in a town called Angel. Inside, he comes across a man who demands payment for the work he just finished in Riverton. When the stranger recognizes Monk he pulls a knife and orders Monk to stop-holding out his six-fingered hand. A struggle over the knife ensues with Monk eventually overpowering the man and pulling out his gun. When the stranger refuses to tell Monk who hired him, Monk threatens to shoot. The stranger doesn't believe that Monk is capable of shooting him, but the fatal shot he gets in the chest would suggest otherwise.
Before Monk can react, the local sheriff arrives, and, after seeing the dead body and Monk holding a gun, arrests Monk. At the station, Monk swears he didn't shoot the man, Frank Nunn, and explains that he would have been crazy to shoot his only lead in Trudy's murder. But the sheriff doesn't buy it - and unfortunately, neither does the judge. In the face of ballistics evidence that indicates that the bullets that killed Nunn definitely came from Monk's gun, Monk's bail is set at $1 million and he's loaded into a transport van to be taken to jail.
But Monk isn't willing to go down without a fight, and while Sheriff Rollins and the van's driver are busy discussing the sheriff's juice-drinking regimen and perfect health, Monk manages to escape. He flees on foot, managing to evade the search dogs, who can't get a scent off of Monk's clothing. Eventually, he makes it back to Natalie's house. She's ready to help her boss, but when Disher arrives to stake out the place, it gets a little complicated. Natalie manages to get Monk out of the house without Disher seeing him, and Monk returns to the sculpture garden to have a look around. He discovers evidence that there was someone hiding in the warehouse that night, someone who was the real shooter.
At the station, Stottlemeyer is working with Sheriff Rollins, who is determined to find Monk by any means necessary, including a wire tap on Dr. Kroger's office, signed off on by his old pal the lieutenant governor. Stottlemeyer receives a call on his cell phone from Monk, who tells the Captain what he's learned: that the man who set him up, the real shooter, was Sheriff Rollins. Monk doesn't know why the sheriff would want to set him up, but he does manage to piece together how. The sheriff broke into Monk's house and switched out the barrel on Monk's gun (and drank some orange juice while he was there). Then he lured Monk to the sculpture garden by stealing the bomb supplies and planting a note that he knew Monk could crack. At the garden, he shot the man, then switched the barrels back while he was arresting Monk so it looked as though the shots had come from Mon's gun. Stottlemeyer is interested in Monk's story, but with no fingerprints or other evidence against Sheriff Rollins, there just isn't enough to exonerate Monk.
When they hang up, Stottlemeyer announces to Rollins that he had just been on the phone with Monk, and that they set up a meeting for that night. Stottlemeyer wants to go alone, but the sheriff insists on sending men. When Stottlemeyer shows up at the foggy pier that night, Monk is suspicious. He and Stottlemeyer argue, and both pull guns. Just as Monk is about to shoot the Captain, Stottlemeyer fires. Monk is hit, and falls off the pier into the water below as a stunned Stottlemeyer, Disher and Sheriff Rollins watch helplessly.