It's demolition day for a parking garage in downtown San Francisco. The city is planning to build a new playground on the site, and the whole community is happy except for Adrian Monk, who's chained himself to one of the garage's concrete posts in protest. Eileen Hill, a city councilwoman who led the effort to demolish the garage, approaches Monk, who explains that for him, the garage is a sacred place since his wife, Trudy, was killed there. The councilwoman agrees to halt the demolition pending a new vote on the matter, and Monk rejoices.
Days later, Monk is called to a murder scene. Two German tourists have been killed on an isolated pier. Monk tries to focus on the case, but the new City Council vote on the garage demolition is happening later that day, and Monk can't wait to get there. Despite his lack of concentration, Monk is able to deduce that the tourists were not killed for money, but for something they witnessed.
With Monk's work at the crime scene done, he hurries off to City Hall, where he meets a newspaper reporter, Paul Crawford, who's there covering Monk's fight to save the garage. Monk also runs into his nemesis, Harold Krenshaw, who happens to be a member of the City Council. Fortunately for Monk, he doesn't need Harold's vote. Councilwoman Hill has assured Monk that she will vote to save the garage, which is enough to give Monk the majority he needs.
Then Monk gets some bad news. Councilwoman Hill is missing, and the vote on the garage measure is postponed. Monk is desperate to find her, as she is the key to saving the garage. He goes to the councilwoman's office and talks to her secretary, Maria Schecter, whose extreme incompetence frustrates Monk. Monk learns that the councilwoman's last meeting before she went missing was with the reporter, Paul Crawford.
Monk talks to Crawford, who admits to meeting with Councilwoman Hill before she disappeared. According to Crawford, there was nothing unusual about the councilwoman's behavior, but he recommends talking to a hot dog vendor who's been holding a grudge against her. Monk follows up on Crawford's suggestion, but the vendor appears to have nothing to do with the councilwoman's disappearance.
Monk meets with Dr. Bell, who suggests that the destruction of the garage could be an opportunity for Monk to move on from the tragedy of Trudy's death. But Monk doesn't want to give up, and instead comes up with a new plan to save the garage without the missing councilwoman.
Monk goes to the councilwoman's assistant, Maria, and convinces her to vote in the councilwoman's place, as Maria is allowed to do under the city's bylaws. While trying to influence Maria's vote, Monk learns an interesting fact: the councilwoman had a second apartment that the authorities don't know about.
Monk and Natalie go to the apartment, which was obviously some sort of love nest. While snooping around, Natalie finds a home pregnancy test that has come up positive. If the councilwoman was having an affair and got pregnant, perhaps her lover is responsible for her disappearance. But with whom was she having the affair?
Unfortunately, any answers won't be coming from the councilwoman, as her dead body has washed up in waters not far from where the German tourists were found. The councilwoman was strangled with a necktie before she was dropped in the water, and in a strange development, medical tests show that the councilwoman was not pregnant. There's a lot to sort out, but Monk is more concerned about the latest City Council vote on the garage issue, which is about to take place.
Monk rushes to City Hall determined to persuade Maria to vote against the garage's demolition. He shows Maria a photocopy of a journal that was found with Councilwoman Hill's body in which the councilwoman writes of her intentions to vote in favor of keeping the garage. Maria is convinced, and she casts the deciding vote to keep the garage standing.
After the vote, Monk is in a celebratory mood, and he invites everyone out for drinks. Because she's pregnant and can't drink alcohol, Maria declines. This reminds Monk of an earlier conversation he had with the reporter, Paul Crawford. When Crawford was asked if the councilwoman had been drinking when he met with her, he said, "She wouldn't be drinking now." It was a strange way to answer the question, and now, after Maria's response to Monk's invitation, Monk knows why Crawford responded that way. Crawford thought that the councilwoman was pregnant.
With that realization, Monk has solved the case. He turns to Paul Crawford, who is at City Hall to cover the garage vote, and accuses him of abducting and killing Councilwoman Hill. Here's what happened. Crawford, who is married, was having an illicit affair with the councilwoman. The councilwoman wanted to deceive Crawford into thinking that she was pregnant with his child, in the hopes that Crawford would end his marriage. To carry out this deception, the councilwoman hired Maria, made her urinate into a cup under the pretense of a drug test, and used Maria's urine to trigger a positive result on a pregnancy test. The councilwoman showed the test to Crawford, but the plan didn't work as she intended. Instead of leaving his wife, Crawford decided to kill the councilwoman. The German tourists must have witnessed Crawford dumping the councilwoman's body off the pier, and they had to die, too.
The final piece of evidence is the necktie Crawford is wearing, which is the same, custom-made style as was used to strangle Councilwoman Hill. Crawford is arrested, but Monk has a new problem. During his summation, he emphasized the fact that the councilwoman only hired Maria because she needed her urine. Insulted, Maria decides to change her vote on the garage, and Harold gleefully calls for another vote. Monk loses. The garage will be demolished.
Having lost a difficult political battle, Monk bids an emotional farewell to the parking garage. But his fight to preserve the memory of his beloved wife wasn't in vain, as the beautiful new playground that will rise in the garage's place will be named after Trudy.