When John Ricca, author of a controversial and unfavorable biography of martial artist Sonny ("the Cobra") Chow, is found dead in his home, all the evidence points to Chow as the murderer like a video of someone dressed in ninja garb leaving the building and some hair that Ricca pulled off his assailant. Unfortunately for Captain Stottlemeyer, his chief suspect has been dead for six years, unless the rumors of him being alive and being held by an Asian Triad is true. Stottlemeyer meets Monk, telling him that they were able to compare the hair they found to some of Chow's blood which he froze years ago. While Monk and Natalie (who's more interested in being reimbursed for her business expenses than in solving the case) visit Chow's former teacher, Master Zee, who claims that Chow died in his arms, Stottlemeyer resorts to having the corpse dug up to prove that, despite rumors to the contrary, Chow is indeed dead.
While waiting for the test to be completed, Natalie asks Monk if he can't afford to pay her why does he have an office that's when he says it's not his office, it's Trudy's. She grabs a pillow out of the coffin and hits him with it. A dental X-ray proving that the corpse is Chow leaves Monk to figure out who tried to frame the dead man for murder.
On an inadvertent tip from Disher, an avid Cobra fan, Monk and Natalie visit the Sonny Chow museum, where Monk finds two important clues--a hairbrush that has been stolen from its case and replaced with a lookalike, and the stamp that the museum proprietor placed on Natalie's hand so that she can return to the museum. Remembering a third clue, a "death pillow" from Chow's coffin that felt harder than it should have when the frustrated Natalie hit him with it, Monk drags her back to the cemetery, but she leaves before he can present his solution to the case. Unfortunately for Monk, the perpetrator overhears himself named as the suspect and knocks Monk unconscious.
Relenting, Natalie returns to the cemetery, discovers that Monk is missing, and calls Captain Stottlemeyer, who knows the "lowlife" perpetrator all too well and rightly deduces what he's done to Monk. Monk wakes up and finds himself in a coffin and buried. He uses the candle Zee gave him to have some light. What looks like the entire SFPD arrives in time to catch the perp, whose fate adds another bizarre twist to the plot, but the real challenge is to find and rescue Monk while he's still alive. Monk, meanwhile, is a lot calmer than the captain: he's spending quality time with his dead wife, Trudy. Monk tells Trudy that he believes one of the grave diggers, Chris Downey, was the one who killed Ricca so that he could frame Sonny Chow. It seems that years ago around the same time Chow died, Downey stole some jewels and hid the jewels in Sonny Chow's coffin and was sure that he could come back for them whenever he wants even years later.
Stottlemeyer, Disher, and Natalie are scrambling to find where Downey buried Monk. Monk continues to tell Trudy that Downey was sent to prison for assault and upon his release he went to dig up the jewels, but during his absence a granite monument was erected in Chow's memory which meant Downey couldn't dig the coffin up quietly so he proceeded to frame Chow by stealing the hairbrush with Chow's hair and killing Ricca and placing it in his hands. Monk is starting to fade but Trudy tells him to hang on. Natalie finds Monk and they dig him up. Before leaving, Trudy tells Monk to close her office and use the money to pay Natalie. When they open the coffin they find him smiling. Later Monk and Natalie clear out Trudy's office, taking everything, even the thumbtacks.