It's the middle of the night at the estate of eccentric record producer Ian Blackburn. Blackburn is in his home studio, working on some songs for his pop superstar wife, Chloe. An alarm goes off, and Blackburn grabs his pet chimpanzee, Darwin, and runs to his fortified panic room where, moments later, police arrive on the scene and blast their way in. They enter to discover an incredibly bizarre tableau: Blackburn shot dead with Darwin the chimp standing over him, covered in blood and holding a revolver.
Stottlemeyer and Disher reluctantly hold Darwin as the prime suspect, but they quickly enlist the help of Monk to determine the guilt or innocence of this most unlikely simian suspect. Sharona immediately takes to Darwin and insists that the chimp couldn't have shot Blackburn. Monk also suspects something more, so he ventures off to interview the security expert who installed the panic room, Kurt Wolff, as well as Blackburn's widow, Chloe. Chloe was clearly sleeping around, and Sharona suspects a connection between Chloe and Wolff, but Monk doesn't have enough facts to move on Sharona's theory.
With Darwin scheduled to be put down, Sharona takes action: she orchestrates a daring late-night rescue at the animal shelter, freeing Darwin from "death row" and hiding him in Monk's apartment. When Monk arrives home, he finds Darwin running amok, but he also finds a key clue: when Monk's landlord shows up to inquire about the ruckus, Darwin goes berserk. Monk remembers a similar reaction when Darwin first met an animal control officer. The common denominator between the landlord and the control officer? They're both bald. Why, then, is Darwin afraid of bald men? Because Darwin witnessed his master, Ian Blackburn, get killed by another bald man - the security expert, Kurt Wolff!
Monk and the police lay a trap. With Kurt Wolff standing nearby, they talk of a supposed damning piece of evidence locked in the panic room - a tape with a recording of the entire murder. They stakeout the panic room, and sure enough, Kurt Wolff shows up in the middle of the night, making his way in through a secret entrance. Wolff had built a secret crawl space that led into the panic room when he installed it for the Blackburns. He was indeed having an affair with Chloe, and the couple conspired to design the panic room - not as a means to protect Ian Blackburn, but as a means to kill him.
Thanks to Monk, the killers wind up in jail, and an innocent chimpanzee is spared from execution.