Steve DeWitt and Amanda Castle are asleep in bed when Steve's dog, a stumpy-tailed Australian Shepherd, wakes Amanda. She goes to the kitchen to cook breakfast and finds a picture of Steve and his wife hidden in a drawer. Amanda, surprised to learn that Steve is married, confronts him. They argue, he shoves her, and she hits her head on a counter. She calls 911, but before she can speak to the operator, she loses consciousness. With Amanda's life in the balance, Steve hangs up on the call and watches her die.
A week later, Monk is with Natalie at her annual family reunion. Despite having his usual issues at the party, Monk has a good time, and leaves feeling sad that he doesn't have a family like Natalie's.
Later, Monk and Natalie are called to the home of Amanda Castle. Amanda, an artist, has been reported missing by her agent, Samantha Allen. Amanda's been gone for days without her dog, Shelby, and Samantha says Amanda would never do that. Monk looks around and concludes that there was a man in Amanda's life. Meanwhile, Animal Control has come to take Shelby away. Shelby seems to like Monk, and Natalie convinces him to take the dog in as a way to cure some of his feelings of loneliness.
Captain Stottlemeyer organizes a volunteer search party at a field near Amanda's house. Monk, Natalie and Shelby watch from nearby. Shelby spots Steve DeWitt in the search party and barks. Steve pretends he's never met Shelby, and pats her belly, noting she needs to go on a diet. The volunteers search the field, and Steve "finds" Amanda's wallet. Monk thinks this was too lucky of a find, and suspects that Steve DeWitt is the guy.
The next day Stottlemeyer does some research and learns that Steve is an art patron, so he could easily know Amanda. They also learn that Amanda called 911 from the vicinity of Steve's townhouse. Steve is the clear suspect.
Meanwhile, some hikers find Amanda's body rolled up in a rug. Monk breaks the news to Shelby that Amanda is dead. Shelby is sad, and Monk completely understands.
Monk and Natalie go to Steve's house to question him about Amanda, and he claims he didn't even know her. Monk notices a brand new rug on the floor. Steve kicks Monk out of the house, but Monk now knows where the rug around Amanda's body came from.
Monk goes home to Shelby, who hasn't been eating. Later that night, Monk walks Shelby, and someone tries to run her over. Monk tells Disher and Stottlemeyer, but they have trouble understanding why anyone would try to kill the dog.
At home, Monk still can't get Shelby to eat. He calls a veterinarian who explains that Shelby is pregnant and in labor at that very moment! Natalie comes over to help. Monk is disgusted by the whole process, but is won over when he sees the first puppy. Monk notices... it has no tail! He calls Stottlemeyer and Disher over and explains that Steve's tailless dog must have fathered Shelby's puppies. It was Steve who was trying to kill Shelby. He had felt the dog's pregnant belly when they searched the field, and feared that when Shelby had her tailless puppies, it would be proof that Steve and Amanda's dogs had met, which would prove that Steve knew Amanda.
Late that night, Steve breaks into Monk's apartment with a knife. Monk wakes up and confronts him - does Steve plan on killing Monk, Shelby and all her puppies? Sensing weakness in Steve, Monk talks him into giving up the knife without a fight.
A week later, Monk is giving away some of Shelby's puppies to Natalie's aunt, but he can't bear to separate them. They're a family. Natalie's aunt agrees to take all of the dogs. Monk says a tearful goodbye to Shelby, and promises to visit her every day.