Harm, Mac and Turner go up against the CIA's top counsel when the agency tries to keep a 1968 Navy sub tragedy, in which 129 men died, classified. In so doing, they must find a way around the CIA's classified information rules in order to follow the orders of the new Secretary of the Navy.

Mac is called in to minimize the damage after a Navy lieutenant blows the whistle regarding deficiencies in a top-secret Navy combat device. When she helps the lieutenant get released from the military, she is furious when she later discovers that he had stolen hi-tech secrets to use in his video-game company.

Meanwhile, Harm is threatened with a lawsuit by an elderly lady and her shady lawyer following a minor traffic accident.

Cdr. Turner gets to hitch a ride on a submarine that is bound for the mideast when it has been discovered that a 10-kiloton nuclear warhead has turned up missing.

Sadik Fahd who held Mac & Webb captive in Paraguay at the end of last season, shows up in Washington, DC and Mac has to wonder what he's up to when he begins to contact her.

Harm temporarily loses his hearing when the car battery on his Corvette explodes while he was working on it.

Harm looks into the crash of a F-14 Tomcat.