In an upscale San Francisco neighborhood, a woman hears a scream from her neighbor's house. She crosses the street to check on her neighbors and finds them brutally murdered in an apparent robbery attempt.
Fourteen years later, that same woman attends a parole hearing for Max Barton, the man arrested for those horrific murders. Testifying at the hearing is Monk, who led the investigation fourteen years ago. Monk wants to make sure that Max Barton stays behind bars, but during Monk's testimony, a young lawyer arrives with some shocking news. A new DNA test of evidence found at the crime scene has exonerated Max, and he will soon become a free man.
Monk is consumed by guilt. He's never made such a grievous mistake - putting an innocent man away for fourteen years. He reaches out to Max, but Max refuses to forgive Monk. Nevertheless, Monk wants to make things right. He promises to help track down Max's ex-wife, Sherry, who left Max during his time in prison. He also sets about the difficult task of finding the real perpetrator of the crime for which Max was falsely convicted.
Monk heads to the fourteen year-old crime scene with Stottlemeyer and Disher, where Monk finds a clue. The murder victims had a dog that died days before they were killed. Perhaps the dog's remains hold some clue as to the true murderer's identity. The dog's body is exhumed.
Meanwhile, Max Barton pays a visit to an old friend named Pauly Flores. Apparently, Max is in fact guilty. He and Pauly committed the murders together fourteen years ago, and Max is concerned that the police will eventually catch up with Pauly, and that Pauly will talk about other jobs the two pulled together. Unwilling to go back to jail, Max kills his old partner.
But Monk still thinks Max is an innocent man, so Monk stays busy catering to the killer's every whim. Monk sets up Max with a job, and Natalie locates Max's ex-wife, Sherry, who's about to get married. Monk rushes to interrupt the wedding proceedings and begs Sherry to give Max one more chance. Sherry agrees, and leaves her groom at the altar to embrace Max.
Everything seems to be back in its place. Max has returned to society and is reunited with his true love. And it's all thanks to Monk. But then a woman approaches. It's the woman who found her neighbors murdered fourteen years ago, and she's insisting that she saw Max Barton leaving that crime scene. Monk reminds her that the DNA evidence is incontrovertible, but she won't give in. And then she says something that Monk never heard her say before. She remembers Max Barton leaving the scene with his hands in his pockets. The killer used a heavy acetylene torch to break into a safe, but the police never found the torch at the crime scene. If the man the woman saw wasn't carrying anything, there had to be another man. That's what nobody accounted for! Max was guilty. The DNA found at the scene didn't belong to Max. It belonged to his accomplice!
Thanks to a clue they found in the remains of the dead dog, Stottlemeyer and Disher have found Max's dead ex-partner, Pauly Flores. It appears to them that Pauly has hung himself, but Monk has other ideas. He recognizes that the belt Pauly used to hang himself belongs to Max Barton. Monk thinks he can nail Max if they can find him. Fortunately, Natalie knows exactly where Max is. He's about to get married to Sherry!
Our gang rushes to the church to interrupt another wedding. This time, Monk convinces Sherry not to marry Max. And, more importantly, he finds the necessary piece of evidence to send Max to prison for the murder of Pauly Flores. When Max used his belt to kill Flores, Max needed a belt for himself. So he took Flores' belt, and is still wearing it at the wedding. The belt is easily identifiable, and Max Barton is arrested. Monk's biggest mistake is corrected, and order is restored to the universe.