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Commander Whitaker is angry to learn that Monk and Natalie are on board his vessel, and orders them to stay out of his way.  To cope with the stress of being underwater in extremely cramped quarters, Monk imagines that Dr. Bell is on board with him.  The imaginary Dr. Bell advises Monk to stay busy with the investigation of Jason Pierce's death.

Monk follows his imaginary doctor's orders and continues to snoop around.  Soon, he makes a connection:  a piece of plastic found in Jason Pierce's quarters matches a bottle of cream soda from a private stash belonging to Commander Whitaker.  Monk theorizes that Commander Whitaker shot Pierce with a crude silencer made from a cream soda bottle.  Monk doesn't know all the details, but he's confident that Jason Pierce was indeed murdered, and that Commander Whitaker was the killer.

Monk continues to gather information.  He learns that a crew member named Jonesy died recently when the submarine ran into an undersea mountain.  The accident was blamed on an outdated navigation chart, but Monk deduces that the accident was in fact Commander Whitaker's fault, and that the commander had covered up his error by replacing a proper, up-to-date navigation chart with an outdated one.  Jason Pierce knew about the switch, and wanted to come clean after Jonesy died, but Commander Whitaker wouldn't allow it, and decided to kill Pierce before he had a chance to talk.

Monk only needs to figure out how Commander Whitaker did it to close the case.  When Monk and Natalie receive a note from a crew member offering to help, they go to a dark compartment for a secret meeting.  When they enter the compartment, the door closes behind them.  Monk and Natalie are trapped, and soon, the compartment is flooded with water.  It turns out they're in a ballast tank, which fills with ocean water whenever the submarine goes into a dive.  It was a trap set by Commander Whitaker, who proceeds to aggressively dive the submarine deeper and deeper in an effort to drown Monk and Natalie.  Lt. Albright realizes what's going on, and forces Whitaker to end the submarine's descent.

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