Aboard the USS Seattle, Commander Whitaker is conducting a surprise drill when he realizes his second in command Lt. Commander Pierce isn't at his post. They go to his cabin and find the door locked, and hear a gunshot. Busting in, they find the lieutenant dead from a self-inflicted head shot with a bottle of vodka on the table.
Albright comes to visit Natalie, having known her husband Mitch. She introduces him to Monk, and Albright says he's needs Monk's help. Albright, the boat's medical officer, insists that Pierce had been sober for nine years and they were going to a game the next nights, so he doesn't believe Pierce committed suicide. Monk is nervous about going anywhere near the water but Natalie convinces him to go.
They get to pier and Monk discovers that Albright is discussing a submarine, not a boat. Natalie reluctantly convinces Monk to come aboard and see Pierce's cabin. Despite his panic, Monk finds a piece of plastic with adhesive and gunpowder on it. An emergency fleet exercise begins and the sub ships out. Monk tries to get out without success. He and Natalie go to the bridge and Whitaker is less than thrilled to have them there. The commander insists that Pierce's death was a suicide and refuses to turnaround. He informs them the exercise will be lasting 4-5 days and refuses to drop them off.
In the officer's mess, Monk starts hallucinating Dr. Bell there trying to help him and being overly praiseworthy. Monk "shows" his clues to Dr. Bell, and insists it isn't suicide. Monk then calls Disher to have him do research on Pierce. Albright shows Natalie to her private quarters and wonders if he's crazy for disputing the official report. He wonders what would have happened if they had ended up together. Albright admits he never married.
Monk goes to see Whitaker, who insists there is no case and Pierce had confessed to him two months ago that he was drinking. Monk notes that there were two drills that day and asks if that's unusual. Whitaker says it is but he did it to make sure the crew was fully trained, and says he doesn't want to see Monk again. As he leaves, Monk secretly takes a plastic bottle of soda and determines it matches the plastic shard he found in Pierce's cabin, and Albright confirms no one else drinks that brand. Monk then borrows Albright's unloaded gun and places the barrel into the bottle's neck. Taping it together, Monk creates a makeshift silencer and believes that Whitaker is the killer.
Later, Monk eats with the crew, who note that Albright has his eye on Natalie and everyone is close on a submarine. Whitaker and Pierce served together in the Gulf War. The sub is hit by turbulence and Monk starts to panic, and the crew note that they hit an undersea mountain a year ago but everyone was cleared of possible incompetence.
Albright goes to see Natalie and they end up kissing, but Natalie says that she can't because of Mitch. Meanwhile, Monk is escorted to his bunk and wonders if they have room for the imaginary Dr. Bell. They note that their former crewman Jones died last Tuesday: the same day Pierce died. Disher confirms that Pierce's family didn't believe he was the suicidal type, but was hiring a criminal attorney. Monk notes some old nav charts and finds an empty chart case. He goes to see Whitaker and inform him he's getting closer to the solution and all he needs is the "how." He tells Whitaker he knows he killed Pierce because of the accident. He convinced Pierce to cover it up by switching charts so he could claim he was given a faulty chart. When Pierce heard that Jones died, he had a change of heart and planned to confess, so Whitaker had to kill him. Whitaker insists that when he's on the ship no one can question him and Monk is having a breakdown.
Monk goes to get Natalie and plans to go check out Pierce's cabin. There's a note under the door that says Monk and Natalie should come alone to a compartment. They go in, and someone locks the door behind them. Meanwhile, Whitaker orders the crew to take the sub down further. In the compartment, Monk and Natalie realize they're in a ballast tank and the ocean starts pouring in. Monk calls for (the imaginary) Dr. Bell while Albright realizes Monk and Natalie aren't in their cabin and finds the note and goes to the ballast compartment but is unable to get the door open. Natalie uses the good-luck belt that Julie made for her as an improvised snorkel and Monk reluctantly puts it in his mouth.
Albright goes to the bridge and insists they surface, showing Whitaker the note. Whitaker reluctantly gives the order to get to the air. Monk, Natalie, and Albright confront Whitaker, and Monk explains that they found the ash of a firecracker in Pierce's cabin's vent. Whitaker forced Pierce to drink and then shot him, then used a cigarette as a fuse to set off the firecracker five minutes after he left for the bridge. He was in the hallway with the others when the firecracker went off, and they've found a thumbprint on the vent. Pierce has Whitaker taken away, and the commander congratulates Monk on a job well done.
Back in port, Natalie invites Albright to see her in December when he returns to port. The imaginary Dr. Bell congratulates Monk on how well he did, and Disher stops by to check in. The real Dr. Bell shows up and plays along with Monk thinking he was there. Monk is astonished that Bell can't remember what happened.