Early one morning, Dr. Kroger's cleaning lady is found stabbed to death in Kroger's office, and the police suspect that one of Kroger's patients could be the culprit. Consumed with the thought that one of his patients would commit murder, Dr. Kroger retires, sending Monk into a complete tailspin.
Monk sets out to uncover what really happened to the cleaning lady. He interviews a fellow patient who had threatened Dr. Kroger in the past, but the patient has a strong alibi. Then, when Monk pays an unannounced visit to Dr. Kroger's house, a rock with a note attached to it is thrown through one of Kroger's windows. The note seems to be from a disgruntled patient, reinforcing the theory that one of Kroger's patients is the killer.
But later, while Monk is paying a visit to a new psychiatrist that Kroger had recommended, Monk makes a realization. The rock that was thrown through Kroger's window came from the courtyard outside Kroger's office. Monk goes to the office and finds Dr. Kroger cleaning out his things. Monk explains about the rock, and Kroger says that his neighbor in the building, a man named Francis Merrigan, is the only other person with access to the courtyard. Monk deduces that Merrigan must be the killer, which is soon confirmed when Merrigan shows up with a gun.
Merrigan ties up Monk and Kroger and throws them in the back of a truck, where Monk explains what happened. Merrigan is a drug smuggler, and while vacuuming in Merrigan's office late at night, the cleaning lady accidentally broke a figurine, dumping heroin all over the floor. The cleaning lady vacuumed the heroin and reassembled the figurine, but when Merrigan arrived at his office later that night, he noticed the missing heroin. He caught up with the cleaning lady in Dr. Kroger's office, killed her, and set up the crime scene to make it look as if a disgruntled patient had committed the murder. The rock through Kroger's window was thrown by Merrigan in an effort to keep the police on the wrong track.
The case is solved, but Monk and Dr. Kroger are in big trouble. Merrigan has taken them to a warehouse, and nobody seems to know where they are. Then, an unlikely hero emerges: Harold Krenshaw, Monk's least favorite fellow patient of Dr. Kroger's. Krenshaw has been following them, and he's made his way into the warehouse. Unfortunately, Krenshaw's obsessive-compulsive behavior gets the better of him at an inopportune moment, and Merrigan spots him. Capt. Stottlemeyer shows up just in time (Krenshaw had called him), and a gun battle breaks out. Dr. Kroger nearly gets shot, but eventually Merrigan is taken into custody. With the true killer under arrest, Dr. Kroger returns to work, and Monk returns to being Dr. Kroger's most difficult patient.