Three homeless men, the Professor, Reggie, and Ike, are in an alleyway a few days before Christmas. As they sing Christmas carols, they wonder where their friend Willie is. He comes running down the alleyway screaming that someone is after him. He claims there's a car after him but they don't see anyone. Willie runs off in terror. The next morning, they go looking for him and find him trapped in a refrigerator, seemingly asphyxiated to death.
Monk is putting up a cardboard Christmas tree at his apartment as Julie and Natalie visit. Monk is his usual cynical self concerning the holidays. Natalie is making soup for Captain Stottlemeyer, who is suffering from arthritis in the back. The Professor, Reggie, and Ike pay a visit and offer Monk $14 in bottles to investigate Willie's death. They insist that he wouldn't have trapped himself in the refrigerator, as the police claim, and think whoever was after him murdered Willie. Monk is more concerned about them getting dirt in his apartment. Natalie invites them to stay for a meal and a panicky Monk finally agrees just to get them out of his apartment. They go to the crime scene and although Monk doesn't get out of the car, he sees enough from a distance to determine that Willie was dead before he ended up in the refrigerator.
Monk and Natalie go to the police station where Disher is handling everything. He agrees to reopen the case and tells them that Stottlemeyer is taking complaints at the front desk because he didn't want to be stuck in his office. Stottlemeyer, walking with a cane, is talking to Mr. and Mrs. Perisi, who say that a picture of a fountain and the word "Drink" magically appeared on their door in chalk. Mrs. Perisi was suffering from a long-term illness but when they found the monastery where the fountain was located and she drank from it, she was cured. Stottlemeyer doesn't believe it and goes to his office only to find that Disher has everything taken care of. Stottlemeyer is depressed not only over his continuing but the fact he hasn't had a date in two years and his son is living with his grandmother and hasn't called. He takes an herbal extract made from chalk but admits that nothing he's taken for his back pains have helped. He goes home and finds the fountain drawing on his door.
Stottlemeyer goes to the monastery and sees other people who have been cured by the fountain, or are preying for a cure. He meets one woman, Kate Doyle, who explains she was the first one who discovered the fountain's healing properties. As Stottlemeyer approaches the fountain, Brother Andrew greets him. They discuss religion and Stottlemeyer admits he used to be a choir boy. Brother Andrew says it's never too late and that perhaps Stottlemeyer needs to make a leap of faith. The captain considers the fountain... and takes a drink.
Monk tries to cash in the $14 in bottles but the clerk informs him that three of the bottles are from Canada and she can't redeem them. Monk isn't happy at being stiffed $0.15 but is distracted when Natalie admits she's invited his three clients to Christmas dinner.
Stottlemeyer goes to see his pharmacist to get his prescription for back pain medicine renewed. The pharmacist, Owen McCloskey, has heard of the miracle fountain and is skeptical, and asks if it's done Stottlemeyer any good. The captain admits it hasn't, and then notices a crucifix hanging on the wall. McCloskey says it belonged to his partner, who embezzled the pharmacy's money nine years ago and disappeared with the loot.
The next morning, Stottlemeyer wakes up and discovers that he's cured.
Monk, Natalie, Julie, and the homeless men meet at Monk's apartment for dinner. Monk is distracted by their dirt and grime, but finally brings up the case. He confirms that Willie was indeed murdered just as they suspected, and that the police have reopened the case. He shows them the three bottles and then realizes that they're the bottles that Stottlemeyer's herbal extract medicine came in. Willie picked up the bottles, meaning that he was at Stottlemeyer's house before he was murdered. They go to the station to tell Disher, but the first thing they notice is the mustache he's grown now that he's in charge. He explains that Stottlemeyer left and didn't say when he'd be back.
Stottlemeyer goes back to the monastery and the fountain. He leaves his cane and his bottle of pills on a pile with all the other discarded crutches and pill bottles.
After getting word that Stottlemeyer's car is abandoned at the monastery, Natalie and Monk visit the place and Natalie suggests that Monk should drink from the fountain to cure his pains. Monk is skeptical of the entire thing and doesn't believe in any miracle. They talk to Kate Doyle and she recognizes Stottlemeyer from the photo they have of the captain. They go inside and meet Brother Andrew, who says that Stottlemeyer has become a monk and taken a vow of silence. Monk wonders if it's some kind of scam and Brother Andrew explains that the fountain is costing them money: they'd hoped to build a classroom on its site but now the fountain has become a holy shrine.
Brother Andrew only allows Monk, a man, into the monastery. He finds Stottlemeyer in the library and finds Stottlemeyer, now clean-shaven and wearing a monk's robe. Monk tries to explain about the murdered homeless man by acting out since he isn't allowed to speak and can't find a working pen. Stottlemeyer finally understands and gestures that he didn't see anything the night of the murder. He gives Monk a small bundle: it's his badge, and a note saying he's leaving for a two-year overseas assignment.
Back at his apartment, Monk wonders what he'll do without his friend and Natalie says that he should drink from the fountain. He refuses and she takes him to the monastery.
Kate Doyle goes to McCloskey's pharmacy and tells him that she can't continue with their plan because some real sick people are visiting the fountain. He says they can't be seen together and slaps her, warning her that they both know what's really under the fountain. She agrees to continue with their plan and he says it's almost over.
Monk and Natalie return to the fountain. Monk still refuses to drink from it. He notices the discarded pile of pill bottles and realizes that most of them are from McCloskey's pharmacy. Kate arrives and sees them examining the pill bottles and confesses. She explains that her fiancé McCloskey found his partner embezzling from the store and killed him.
Once they have the full story, Monk and Natalie disguise themselves as monks and sneak into the monastery. They find Stottlemeyer attending a ceremony. Monk is forced to chant out what happened: McCloskey killed his partner and buried him in the monastery. The monks built a fountain but didn't find the body. Nine years later the monks decided to build a classroom on the site. To stop them, McCloskey made his own patients sick by tampering with their prescriptions and then drew the fountain on their doorsteps. Kate started the stories and McCloskey would then "cure" his customers by giving them the proper medication. Willie saw McCloskey drawing the fountain on Stottlemeyer's door and the pharmacist killed him to protect his secret.
They go outside with Stottlemeyer, who realizes the whole thing was a hoax. The captain admits that he still feels as if something has changed in his life. The police arrest McCloskey and the three homeless men thank Monk. The captain admits to Disher that he feels ready to start over again, and gets a call from his son Jared.
Later, Monk goes to the fountain with a glass. He gets himself a glass of water and then just stands there, considering it.
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