Bertrum Gruber receives the $250,000 reward for tipping the police in the right direction. After the press conference, Natalie finds that her car's tires have been slashed. After having the tires replaced, she and Monk return to his apartment and find Stottlemeyer there. The Captain advises Monk to keep his profile as low as possible and not to align himself with the commissioner or with the mayor. Leaving Monk, Natalie gets pulled over as her trunk is open. The next morning, Monk and Natalie find Porter to have replaced the Charlie Herrin cases with the other four open murder cases (Allegra Doucet, John Yamada, Diane Truby and Scott Eggers).

Monk is called in to investigate the death of a music producer who was shot in the back, chest and his head in a room locked from the inside. In the room, the police found the dead man's pet chimpanzee, Darwin holding the murder weapon in his hand.

Monk suspects a '90s radical man named Winston Brenner to be connected to the city-wide blackout which resulted in three deaths. However, Brenner is supposed to have died in 1995.

While Monk was investigating a case involving a female victim whose body was cut up with a chainsaw, he accidentally erases several years' worth of crucial computer files. As a result of that, the commissioner revoked Monk's private practice license. Monk struggled to look for a new job.

A mob godfather, Salvatore Lucarelli, hires Monk to investigate the death of five members of the West Coast Mafia during a shoot out in a barbershop. Agent Colmes of the FBI offers Monk the reinstatement on the police force if he helps him to bring down the mafia gang.

Sharona suspects she is suffering from a mental breakdown when she has several frightening encounters with a blood-soaked man that no one seems to believe exists.

Monk is called in to investigate the death of Edna Coruthers, a model employee at Mega-Mart by the store's security chief, who turns out to be his disgraced ex-partner, Joe Christie. At first, Monk was reluctant to help Christie, however, later he agrees and began to go undercover as a store clerk.

Trudy's father, Dwight Ellison, pays Monk a visit and invites him to spend the week with him and his wife, Marcia. He also asks Monk to help him to investigate Roddy Lankman, the game show host who seems to be involved in a conspiracy to allow one of his contestants, Val Birch, to win every game.

Feeling depressed and helpless after Captain Stottlemeyer is shot by an unknown assailant, Monk decides to try a new medication that eliminates his phobias. But it also makes him unbearably egotistical.

Sharona has remarried her ex-husband and moved to New Jersey, Monk still can't t find a new assistant after three months. Meanwhile, Natalie Teeger who is a widow with an eleven-year-old daughter, kills an intruder in her house in self defense. She is baffled as this is the second time someone broke into her house in the past few days. Captain Stottlemeyer suggests she go to Monk for help.

John Ricca, an author of a controversial and unfavorable biography of martial artist Sonny Chow, is found murdered in his home and all the evidence seems to point to Sonny as the murderer. However, Sonny has been dead for six years. Meanwhile, Monk disagrees with Natalie regarding the reimbursement of her expenses.

Monk witnesses a Chinese mob killing and is forced to take refuge in an FBI safe house out in the forest. After hearing a man screaming, Monk is convinced a murder has taken place nearby - but the agent assigned to protect him isn't so sure.

Monk, Natalie, and Julie are stuck in a traffic jam after a multi-car collision blocks the freeway. Monk got out of the car to investigate and discovers that the man in the overturned Volkswagen that caused the collision was murdered and didn't die from the accident. His body was placed in the car in order to make his death look like an accident.

Monk receives a call from a drunken Stottlemeyer, who is in Las Vegas with Disher for a fellow officer's bachelor party. Stottlemeyer suspects that the casino owner has murdered his wife. However, when Monk and Natalie arrive in Vegas the very next day, Stottlemeyer can't remember anything that happened the previous night.

Suspicion falls on Natalie's opponent in the election, Harold Krenshaw, whom Monk knows as a fellow patient of Dr. Kroger's. Although Monk thinks that Krenshaw is lying about his friendship with Dr. Kroger and Krenshaw admits to being an excellent shot, Monk is sure that Krenshaw is innocent because he wouldn't misspell Natalie's name.

A 22 month old toddler, Tommy Graser, finds a severed finger and gives it to a policeman. Monk is called in to investigate and together with Tommy, they walk through the park, trying to retrace the small child's steps.