Natalie is driving back from a friend’s wedding, and unhappy at Monk. She’s mad that he begged her to take him with her so he wouldn’t be alone, but spent the entire time avoiding people. Her car breaks down as they’re crossing a bridge and she tries to figure out what’s wrong. As Monk goes nearby and tries to get a phone signal, he sees a glowing object fly overhead.
The next morning, Natalie gets the car towed to the nearby town of Vintonville. The mechanic, Boom Boom, asks the mechanic if anyone in the area has ever seen a UFO. Boom Boom says they haven’t but admits he’s seen a ghost once. Monk doesn’t believe him and bluntly says that he’s dumb. Boom Boom takes offense and hikes up his estimate for repairing Natalie’s car. Natalie complains that Monk doesn’t have any empathy and tries to get him to apologize without success.
Natalie calls Stottlemeyer to tell him they won’t be backing time for the seminar Monk is supposed to be attending, and to inform him of what Monk saw. Stottlemeyer half-jokingly wonders if Monk might be an alien. Meanwhile, Monk goes to talk to Sheriff Fletcher, who is taking a statement from Dolly saying that her neighbor Marjorie has disappeared. Fletcher figures that Marjorie is just out hiking and there’s nothing to be concerned about. He then turns to Monk, who reluctantly explains that he saw a UFO without actually saying the word and making himself look like a crank. He finally brings himself to do it and Fletcher sarcastically says that it’ll make a pleasant change from investigating important crimes.
That night, Monk stars seeing imaginary UFOs everywhere as he and Natalie go back to their hotel room. As the bellboy at the Sleep Inn greets them, Monk sees the UFO again, rising above the tree line. This time Natalie and the bellboy also see it. By the next morning, UFO enthusiasts have learned about the sightings from the Internet and are assembling at the hotel. They want to talk to Monk, who would rather not talk to anyone at all. However, when he begins to act like… well, Monk, they wonder if he might be an alien. They show him their stomachs and ask to see his belly button to prove he’s human. Monk refuses but, fortunately for him, the enthusiasts learn that someone has found the UFO’s landing site. After they leave, Monk and Natalie go to see Boom Boom, who fakes stupidity and tells them that it will take longer than he estimated to get Natalie’s car fixed.
In the desert, the UFO enthusiasts search the desert for the UFO and find a woman’s corpse and call Fletcher, who asks Monk to help out. The woman’s corpse was torn off by coyotes, which dragged her body far out into the wilderness. As Monk examines the corpse, Fletcher explains that Marjorie inherited a small fortune a few years ago and has spent it on various hobbies and interests. She liked to go hiking through the area and Fletcher figures she injured herself and her body was dragged to the landing site by wild animals. However, Monk checks her clothing and boots and realizes that someone dressed her after she died.
Monk, Natalie, and Fletcher go to Marjorie’s house. Her brother Kyle is in town and lets them in. As Monk goes over the house, Kyle explains that he lives in San Diego and he hasn’t seen Marjorie in a while. As he talks about how his business went bankrupt a year ago, Monk finds double-sided tape on the floor. He realizes that there was a rug there and someone removed it. Monk also finds a plastic clothing stay on the floor and concludes it was from Marjorie’s new clothing. The detective realizes that someone killed Marjorie there and dressed her, and then took her out using the rug to carry the corpse.
The UFO enthusiasts show up at Marjorie’s house, looking for Monk. He quickly gets by them and goes out to the desert with Fletcher and Natalie to examine the crime scene. An unseen sniper opens fire on them, shooting the sheriff in the leg. He also shoots the sheriff’s jeep, destroying the engine and the radio. With no other way to get help, Monk has no choice but to walk across the desert to get assistance while Natalie stays with Fletcher. He starts hallucinating, complaining that dirty has finally defeated him. As he treks across the desert, he finds batteries, eyeglass wipes, and engine lubricant cans lying in a pile. Despite his condition, he still has enough presence of mind to pick them up and put them in a plastic evidence bag. As he continues, Monk promises God that he’ll be nice to people from now on as long as he gets rescued. Over the next hill, Monk finds the UFO enthusiasts.
The enthusiasts call the hospital and get Monk and Fletcher to the hospital. As he recovers back at the hotel, Monk explains the case. Here’s what happened: Kyle went to Marjorie’s house and killed his sister. He needed to make it look like an accident so he dressed her in hiking clothes and took her body out to the desert. However, when nobody found the body because the coyotes moved it, Kyle realized his plan was in trouble. He needed someone to find the body so Marjorie would be reported dead. When Kyle let them in, Monk remembers that he drove a van with the logo of a hobby store on the side. Kyle owned a hobby store before it went bankrupt. So when Kyle needed someone to find the body, he used supplies from his model hobby store to make a fake UFO. He then sent it up into the air and Monk saw it. Kyle used it again publicly at the hotel when Monk wouldn’t tell people what he saw. Eventually the UFO enthusiasts found Marjorie’s corpse, just as Kyle planned.
As Fletcher goes to arrest Kyle, Monk goes outside to gently and sympathetically tell the UFO enthusiasts that there are no such things as UFOs and they can go back to their regular lives. Natalie is surprised and pleased that he finally took her advice. However, they don’t have regular lives and are disappointed that he’s shattered their fantasies. Realizing that, Monk tells them that there actually are UFOs and he’s an alien from outer space sent to cover up the whole thing.
Much later, Natalie arrives and tells Monk that Kyle finally confessed to his sister’s murder. She has to admit, however, that she still has a few doubts about Monk himself. When she tries to see his belly button, he hides in the bathroom.