On a deserted beach, Captain Stottlemeyer stands alone, waiting. And who should emerge from behind the rocks but Adrian Monk, last seen falling into the bay after being shot twice in the chest by Stottlemeyer. Thanks to a bulletproof vest, Monk is only a little worse for wear. But, as the two friends had planned, the rest of the world thinks he’s dead. So Stottlemeyer hands Monk some dry clothes and send him off with instructions to lie low until they can figure out what Sheriff Rollins is up to.

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.

Bennie, the cantankerous owner of a Bennie’s Junk ‘n’ Stuff, is talking to his assistant. He tells the reluctant young man to set up traps around his property to protect against intruders, and though concerned about the danger, Hector dutifully obliges. Later that evening, Hector’s fears turn out to be well-founded: an armed intruder sets off a trap, and ends up with a fatal gunshot to the chest. While examining the crime scene the next day, Monk makes some important discoveries and realizes that the intruder must have had an accomplice. Natalie also spots something of interest: a painting set, complete with a stack of blank canvases. Since Dr. Kroger had only that morning suggested that Monk pick up a new hobby, Natalie urges him to buy the paint set – and Bennie the Junkman makes an offer they can’t refuse.

When Monk and Natalie are waiting outside a crime scene, they happen to overhear a call on the police radio mentioning a homicide. The victim’s name? Julie Teeger. Natalie, understandably terrified to hear her daughter’s name, hops into Captain Stottlemeyer’s brand new car and speeds off to the scene of the crime. The victim doesn’t turn out to be Natalie’s daughter, which is good news for Natalie, though not for the dead Julie Teeger’s distraught husband, to whom Stottlemeyer makes a promise that he’ll track down the killer. But just as Monk is in the middle of examining the crime scene, the police hear another call about a dead bicyclist. The second victim’s name? Julie Teeger! This death appears at first to be a hit-and-run accident, but once Monk takes a closer look, he realizes something bizarre is going on: someone in San Francisco is killing Julie Teegers.

It’s nighttime, and two cops are outside the West Bay Trust bank, writing a parking ticket for an illegally parked SUV. They mention that the bank had just been robbed the day before but tonight there’s no evidence of trouble. As the cops drive away, however, a glimpse inside the bank proves that not everything is as it seems: four people are trapped inside the bank’s vault. The unfortunate foursome? Monk, Natalie, Capt. Stottlemeyer and Lt. Disher.

While out shopping, Natalie and Monk spot the parents of a recently murdered girl named Amanda Clark, and Monk begrudgingly takes the case – before the Clarks even ask. Monk and Natalie visit the crime scene with Capt. Stottlemeyer and Lt. Disher and Monk speaks to Tom Donovan, the man who found Amanda Clark. Donovan says he saw Amanda being forced down and stabbed by a group of people – one of whom was clearly the leader. When the killers spotted Donovan they took off in their silver van, leaving Amanda with ten stab wounds and a symbol of a sun carved into her chest. As he was driving Amanda to the hospital, Donovan heard her day, “He found me. Father found me.” Then she died.

On their way to Doctor Kroger’s office, Monk, Natalie, and Julie get stuck in a traffic jam. A man dressed as Santa Claus is throwing toys from a rooftop, and the street is clogged with people trying to catch the gifts. Annoyed by the delay, Monk gets out of the car and races into the building to stop Santa. Moments later, gunshots are heard, and Natalie and Julie rush up to the roof. What they see stuns them both – Santa’s been shot, and Monk is holding a smoking pistol!

One day, a mysterious woman in the street grabs Monk’s attention. Monk has never met the woman before but she seems strangely familiar and he feels compelled to chase her for two blocks before losing track of her. The encounter so haunts Monk that he can’t sleep for days. Growing desperate, Monk takes Natalie’s advice and decides to go for a late night walk, during which he sees the mystery woman for a second time. This time, the woman is driving a taxicab. Monk tries to stop her but she eludes him once again. Then, Monk hears angry voices coming from an alley. He follows the noise to a restaurant window where he sees an apparent drug bust going down. An undercover cop is pointing a gun at two men: a longhaired drug dealer and a bookish man. A fight ensues and the undercover cop is shot dead by the drug dealer. The bookish man and the drug dealer run away. Monk rushes to a pay phone and reports the crime but by the time Stottlemeyer and the police arrive on the scene, there is no body, no blood and no sigh of a struggle. Stottlemeyer thinks that Monk, in his sleep-deprived state, is seeing things and suggests that Monk go to a bar, have a drink and get some sleep.

A woman hears a scream from her neighbor's house. She crosses the street to check on her neighbors and finds them brutally murdered in an apparent robbery attempt. Fourteen years later, that same woman attends a parole hearing for Max Barton, the man arrested for those horrific murders. Testifying at the hearing is Monk, who led the investigation fourteen years ago. Monk wants to make sure that Max Barton stays behind bars, but during Monk's testimony, a young lawyer arrives with some shocking news. A new DNA test of evidence found at the crime scene has exonerated Max, and he will soon become a free man. Monk is consumed by guilt. He's never made such a grievous mistake – putting an innocent man away for fourteen years. He reaches out to Max but Max refuses to forgive Monk. Nevertheless, Monk wants to make things right.

One morning in San Francisco, an amazing thing happens. The Frisco fly, a masked daredevil who climbs the city’s building while avoiding the police, falls during one of his stunts. Onlookers rush over to the fallen Fly, who turns out to be Monk’s bitter rival, and fellow patient of Dr. Kroger’s, Harold Krenshaw. Miraculously, Harold survived the accident and is rushed to the hospital. Meanwhile, Monk is with Capt. Stottlemeyer on a secluded stretch of road investigating a burned out car wreck. There’s a dead man behind the wheel and every piece of identifying information has been removed from the victim and his car. It looks like vehicular homicide but Monk thinks the victim’s death was accidental and that someone who happened upon the scene set the car on fire sometime after the victim’s death. But why would someone do such a thing? Monk is soon confronted with an even more baffling question when he hears the news about Harold Krenshaw. How can Harold, who has more fears and phobias than Monk, be the Frisco Fly?