Shelby the dog wakes up his mistress Amanda Castle, who is in bed with her lover Steve DeWitt at his townhouse. Amanda goes out to make breakfast and opens a drawer, only to discover that DeWitt has photos of his wife and a wedding ring hidden away. She confronts DeWitt, who claims that he's in the process of getting a separation and it's been over for a long time. She grabs the photos and tries to destroy them and DeWitt struggles with her. Amanda hits her head on the counter and tries to call 911, but then passes out from her head wound. DeWitt hangs up the phone and looks down at Amanda.
Monk goes to Natalie's family's 25th anniversary reunion. Natalie's niece wonders if he has any family of his own and he doesn't answer. Monk participates as best he can but stands by himself even when Natalie invites him over to join in the group photo. Afterward, he goes home and eats alone.
The next day, Stottlemeyer calls Monk in to investigate Amanda's disappearance. As they arrive, Monk tells Natalie that she should consider herself lucky she has family. They meet with Samantha Austin, Amanda's agent, who tells them that Amanda has been missing since the last weekend. She's sure that Amanda wouldn't have left without her medication or her dog Shelby. Monk sees the dog and panics briefly, and then examines the house. He notices that someone left an eyeglass case but Amanda doesn't wear glasses. Samantha doesn't know if Amanda was dating anyone, but admits that Amanda was a private person. Monk notices a new painting and the subject is wearing glasses and naked. As he looks around, Shelby follows him and licks his hand. Natalie points out that Shelby likes him but Monk tells it to go away. An animal control officer comes by to get Shelby and Natalie suggests that Monk adopt the dog until they find Amanda. Monk is reluctant to do so until he learns that Shelby will be killed in a month if no one claims her.
Monk takes Shelby around and shows her the one spot that she can stay in. He soon discovers that dogs shed and scratch. When he discovers Shelby drinking out of the toilet, he runs in terror.
Stottlemeyer and Disher organize the locals to search for Amanda and Monk and Natalie come along to assist. Monk admits he couldn't leave Shelby alone in his apartment. He's forced to admit that there are moments with Shelby that aren't totally unbearable. Shelby pulls Monk over to DeWitt, one of the search party members, who says that Shelby probably smells his dog on him. The search party goes through the field looking for graves and DeWitt finds Amanda's wallet. There's a note in it saying that she's meeting with her ex-husband. Monk examines the wallet and notes that DeWitt has glasses. He addresses the volunteers and tells them that one of them killed Amanda. He asks the guilty party to raise their hand but no one does. However, Monk insists that DeWitt is guilty. He points out the wallet has no rust on it so DeWitt must have planted it, and he didn't look around like everyone else did when Monk accused one of them of killing Amanda.
Back at the station, Monk worries about the time and wants to make sure he's back at his apartment to be with Shelby. He keeps praising Shelby and Natalie gives him a sha-poopie. Monk notes that he's trained the dog to hold it in, but Disher and Natalie warn that eventually Shelby is going to no longer hold it in. Stottlemeyer confirms that DeWitt signed in using a phony name but has confirmed his real identity. He's an industrial engineer and his wife owns a $2 million brownstone. DeWitt hangs out at art galleries and it's possible he was her patron. Disher gets an idea and tries to eliminate everywhere that Amanda couldn't be buried. The police records arrive and confirm that Amanda made a 911 call, but they can only place it within ten blocks of DeWitt's townhouse. Monk is eager to leave and take care of Shelby, and Stottlemeyer wonders if his friend has a girlfriend.
Monk arrives home, dons protective gloves, and gives Shelby some ice cream for dessert. Later he walks Shelby and tries to get her to fetch a ball. He finally realizes it would work better if he takes the ball out of the bag.
A father takes his two sons hiking in the hills. The boys find a rug… and Amanda's corpse inside.
Monk is vacuuming Shelby when he gets word that Amanda is dead. He tries to explain to Shelby that Amanda has gone to a farm and is happy chasing rabbits, and sympathizes with Shelby over her loss.
Monk and Natalie talk to DeWitt, who claims he never met Amanda and he volunteered to help in the search out of civic duty. Monk notices that the floor in the kitchen has been recently cleaned and Natalie observes that he has a lot of paintings. As DeWitt ushers them out, Monk notes that he has a new rug. DeWitt's wife comes in with their dog, an Australian Shepherd of a breed that's born tailless. She notes that she was in London the previous week during a three-month trip when DeWitt bought the new rug.
Monk arrives home where Natalie's niece is taking care of Shelby. He notices that Shelby hasn't eaten and then takes her out walking. As they cross the street, a driver deliberately tries to run Shelby down and Monk saves her just in time. He tells Stottlemeyer about the incident and insists it wasn't a coincidence, but he can't positively identify DeWitt. Monk is worried because Shelby is acting strangely. Monk goes home with Shelby and calls a veterinarian to describe the dog's symptoms. The veterinarian explains that Shelby is in labor.
Monk calls in Natalie and covers the apartment in newspapers. Natalie insists that he opened his heart and he shouldn't close it now, but he tries to get Shelby to stop. It doesn't work, and even he's touched by the birth of the puppies. Monk is also intrigued, because he notices that the puppies don't have tails. They call over Stottlemeyer and Disher, and Monk explains that DeWitt had an affair with Amanda while his wife was gone. Their dogs also hooked up. When DeWitt participated in the search, he noticed that Shelby was pregnant and realized it would prove that he had met Amanda.
Shelby finally finishes giving birth and Stottlemeyer and Disher put out an APB on DeWitt. After everyone leaves, DeWitt breaks into the apartment. Monk is sleeping on the couch and tells him that he's too late and Shelby has already had the litter. He asks DeWitt if he plans to kill Shelby, the puppies, and Monk. Monk believes that DeWitt is no killer and that Amanda's death was an accident. He tells DeWitt not to make it worse by adding murder to manslaughter and obstruction. Monk takes the knife and both men admit the puppies are beautiful.
Later, Natalie gives away one of the puppies to her niece but Monk realizes he can't split them up. Natalie knows he's thinking about his own family but Monk insists that they can't be split up. Natalie's sister offers to take the whole family, including Shelby. Monk agrees and insists on visiting every day. He tells Shelby she'll never be alone today and Shelby puts a paw on his knee. Monk takes off his glove and cautiously touches Shelby for the first time.