During the investigation of a murder in a junkyard, Captain Stottlemeyer punches a cop named Ryan Sharkey, who claims to be having an affair with the captain's wife, Karen. The only witness to the murder, a homeless man named Gerald or Jerry, has disappeared, but Stottlemeyer suspects businessman Michael Karpov, who is facing charges for money laundering and had a motive for killing the victim, who was scheduled to testify against him. Removed from the case and ordered to take anger management classes, Stottlemeyer asks Monk and Natalie to follow his wife, whom he suspects of lying about her whereabouts. They discover Karen having lunch with a man but are only able to photograph him from the back before being interrupted. Meanwhile, the homeless witness has been stunned and thrown from the third floor of a building but survives the fall, thanks to a corrugated refrigerator carton. Disher places Karpov in a line-up otherwise composed of police officers, including Sharkey, but Stottlemeyer, still enraged at Sharkey, disrupts the line-up before the procedure has been completed. An apple provides the clue that Monk needs to solve the murder case, and Karen reveals the identity of the mystery man she had lunch with. Unfortunately for the captain, it isn't Sharkey.

Julie and her friends hire Monk to look into the suspicious death of their basketball coach.

A friend of Natalie's ex-husband seemingly commits suicide aboard a locked cabin on a submarine. Monk agrees to investigate, despite his phobia about being on--and beneath--the water.