While out shopping, Natalie and Monk spot the parents of a recently murdered girl named Amanda Clark, and Monk begrudgingly takes the case - before the Clarks even ask.
Monk and Natalie visit the crime scene with Capt. Stottlemeyer and Lt. Disher, and Monk speaks to Tom Donovan, the man who found Amanda Clark. Donovan says he saw Amanda being forced down and stabbed by a group of people - one of whom was clearly the leader. When the killers spotted Donovan they took off in their silver van, leaving Amanda with ten stab wounds and a symbol of a sun carved into her chest. As he was driving Amanda to the hospital, Donovan heard her say, "He found me. Father found me." Then she died.
According to Stottlemeyer, Donovan's story checks out. Amanda had left a cult called Siblings of the Sun over a year before her death, and had apparently been so terrified that Father, the leader of the cult, would find her that she changed her name and went into hiding, working off the books as a prostitute. Donovan was able to pick Father, formerly a used car salesman named Ralph Roberts, out of a lineup, but there still isn't enough evidence to charge the cult leader. The problem is, Father has about a hundred witnesses to back up his alibi for that night, and almost as many lawyers ready to sue the police. Since the police won't send anyone in to infiltrate the cult, Monk offers to go undercover, an idea Stottlemeyer swiftly rejects. It's agreed instead that Natalie, who won't pose such as easy target for the cult, will be the one to infiltrate it.
The only problem is, the Siblings of the Sun don't want her. When Natalie approaches the Siblings at one of their recruiting stations, they quickly lose interest in her when they find out she has a daughter. Before Natalie can do anything about it, Monk steps in and the cult leaders whisk him off to their private ranch.
On the ranch, Monk gets a tour of the grounds, which are filled with serene cult members, and speaks with Brother Zach, who had been stationed in front of Father's cabin the night of the murder on security detail. Brother Zach tells Monk that he is sure Father never left his cabin that night - he claims he could hear Father talking to God all night, and even heard his microwave beeping.
Stottlemeyer is concerned when Natalie arrives at the station alone and announces that Monk has joined the cult - and it turns out he has good reason to be. Back at the Siblings of the Sun ranch, Monk seems to be falling under Father's spell. Soon he is wearing yellow and selling flowers at the airport, just like all the other cult members. When Monk visits Father's cabin, Monk finds a syringe cap on the floor and notices that Father seems to have trouble bending over. But when Father confronts Monk about being a police-planted mole, all Monk can focus on is being allowed to stay at the ranch. He begs Father to let him stay at the ranch, where he doesn't have to think, and professed his loyalty and gratitude.
Father lets him stay, with one little proof of gratitude: Monk's savings. To prove his allegiance to the Siblings of the Sun, Monk visits the bank with several of the other cult members. Just as he is handing over a check, Natalie, Stottlemeyer and Disher pull up and force Monk into their car. They bring him back to Natalie's house, where with Dr. Kroger's help they try to deprogram him. Dr. Kroger is finally able to get through to Monk by reminding him of Trudy. Moments later, Dr. Kroger's beeper goes off and Monk realizes something; he's solved the case.
Monk, Natalie, Stottlemeyer and Disher pay Tom Donovan a visit, where Monk accuses Donovan of murdering Amanda Clark. Father's had an alibi for the night of the murder, an alibi he couldn't reveal for fear of ruining his image as the Eternal One; a doctor was paying him a secret visit to give him a shot for his back pain - that explains the syringe cap Monk had found, and the beeping sound Brother Zack had mistaken for a microwave. Monk's theory has been corroborated by Father's doctor, which leaves only one question: why would Donovan lie and pretend he'd seen Father stabbing Amanda? The answer? To deflect the blame off himself.
Donovan's wife refuses to believe that her husband is guilty of murder, and hands Stottlemeyer a traffic ticket her husband had just received in the mail, which includes photos of Donovan with Amanda sitting in the passenger seat with her seatbelt on. Donovan claims that the photo was taken on the way to the hospital, but when Monk examines the car he notices that there isn't any blood on the seatbelt. He announces that the photo was actually taken before Amanda was stabbed - in fact, it's the reason she was stabbed. Donovan had hired Amanda, and as they were driving he realized their photo had been taken by a traffic camera. He knew his wife would see the photos, so to come up with an explanation for why he had another woman in his car, he murdered Amanda and then pretended to try to drive her to the hospital. He knew about her history with Siblings of the Sun, so he pinned the murder on them. And he probably would have gotten away with it too.
After revealing the truth about Donovan, Monk gets a chance to set the record straight about one more thing: Father's supposedly perfect health. When Father and some of the Siblings confront Monk and Natalie on the street, Monk exposes Father's deception about the back problems and secret doctor's visits. Monk also declines Father's invitation to return to the ranch and walks away, leaving some stunned Siblings - and his cult days - behind him.