Private detective Adrian Monk has brains, instincts, a photographic memory and more than a few obsessive-compulsive disorders. These traits, his ever-present handy wipes and his devoted assistant, Natalie Teeger, help him as he solves cases involving amnesia, betrayal, first loves, true loves and of course, murder. Along with Capt. Stottlemeyer and Lt. Disher, Monk is on the case and more germaphobic than ever.
When an officer dies after drinking poisoned wine sent to Captain Stottlemeyer as a Christmas gift, the captain suspects Frank Prager, who tried to shoot him outside a bar several months earlier. Searching the crime scene for clues, Monk notes that the bullet holes seem to form a pattern, but neither he nor Stottlemeyer can figure out the message they're intended to convey. After trying unsuccessfully to talk with Prager's young daughter, Monk goes under cover as Santa Claus. This time he learns that Prager is hiding in a church with ""three ladies"" in front of it. But when Prager is caught and interrogated, it's clear that he had nothing to do with the poisoned wine. With the other suspects on Disher's list also eliminated, Monk and the captain are back to square one. But when Monk opens the card accompanying his gift from the Christmas party, he finds the clue that solves the case.
Monk is facing a crisis: he's down to five shirts. But Inspector No. 8, the only shirt inspector who can meet Monk's criteria for perfection, is not up to her usual standards. Sensing that something is wrong, Monk visits No. 8 on the job. The inspector, Maria Ortiz, informs him that her son, Pablo, has been imprisoned for murdering a fashion model, but she's certain that he's innnocent. Monk is chiefly concerned about his shirts, but Natalie persuades him to talk to Pablo because ""it's the right thing to do."" The conversation uncovers just one clue: Pablo can't read English. When Monk realizes that the killer must have been able to read an emergency exit sign, he's convinced that Pablo is innocent despite the DNA evidence used to convict him. With Stottlemeyer and Disher in tow, Monk and Natalie attempt to talk to the model's former roommate and the fashion designer she worked for, Julian Hodge. But now there's a new problem: Hodge wants thirteen-year-old Julie to model for him. Watching the rehearsal for a fashion show in which Julie will make her debut, Monk discovers a clue that points him to the real killer. When another supermodel is found dead, it's imperative that Monk find new evidence to prove his suspect guilty of both murders and set Pablo free--and for Natalie to get Julie away from the person committing the murders.
During the investigation of a murder in a junkyard, Captain Stottlemeyer punches a cop named Ryan Sharkey, who claims to be having an affair with the captain's wife, Karen. The only witness to the murder, a homeless man named Gerald or Jerry, has disappeared, but Stottlemeyer suspects businessman Michael Karpov, who is facing charges for money laundering and had a motive for killing the victim, who was scheduled to testify against him. Removed from the case and ordered to take anger management classes, Stottlemeyer asks Monk and Natalie to follow his wife, whom he suspects of lying about her whereabouts. They discover Karen having lunch with a man but are only able to photograph him from the back before being interrupted. Meanwhile, the homeless witness has been stunned and thrown from the third floor of a building but survives the fall, thanks to a corrugated refrigerator carton. Disher places Karpov in a line-up otherwise composed of police officers, including Sharkey, but Stottlemeyer, still enraged at Sharkey, disrupts the line-up before the procedure has been completed. An apple provides the clue that Monk needs to solve the murder case, and Karen reveals the identity of the mystery man she had lunch with. Unfortunately for the captain, it isn't Sharkey.
Low on cash because they haven't had a homicide to investigate in three weeks, Monk and Natalie search for the stolen Alexander Diamond, hoping to win the million-dollar reward. Unfortunately, they have competition in the form of a retired Scotland Yard investigator, a bounty hunter, and a gadget-loving private detective, all of whom want the reward money for themselves. Monk quickly figures out that the heist was an inside job and that one of the robbers was under five feet tall, short enough to hide inside a roll-top desk. He also discovers a clue linking a perpetrator to a transcendental meditation retreat. With their competitors close behind them, Monk and Natalie head for the retreat, where they find the thief, who is unfortunately dead. Meanwhile, Disher is having to interrogate a strange young woman who keeps turning herself in for such ""crimes"" as stealing pens or murdering a hamster. Monk tells Natalie that he's solved the case and they race to the police station with the other detectives following. The only thing left is to find the diamond before their competitors do.
When Captain Stottlemeyer suspects that a suicide is really a murder, Monk confirms his suspicions by discovering that the victim, Joanne Raphelson, was too short to have used the stool she supposedly stood on to hang herself. But the next clue, the remains of an olive, a cherry, and a cocktail onion on a stirring stick, leads Monk to suspect that the murder was committed by an astronaut, Steve Wagner. A little research reveals a motive--Joanne was about to publish a book revealing that Wagner had abused her five years earlier. Now all Monk has to do is to prove that Wagner could commit the murder when he was in outer space.
During the investigation of an armored car heist involving the deaths of two drivers and the theft of valuable government bonds, Lt. Disher tries to convince Captain Stottlemeyer that he witnessed a murder while under anesthesia in the dentist's office. When one of the highjackers, Denny Jardeen, is found murdered, Disher insists that Jardeen is the man he saw Dr. Bloom and his assistant kill while he was sedated. Stottlemeyer still thinks that Disher was hallucinating, and Disher angrily leaves the force, deciding to revive his high school rock band, the Randy Disher Project, as an alternate means of earning his living. Meanwhile, the only clue to Jardeen's murder is two pairs of bruises each ten inches apart on the dead man's chest.
Monk is summoned to jury duty against his wishes and must solve two crimes: he has to convince the jury the defendent is not guilty, and solve the mystery of a corpse outside the jury room's window.