Admiral Chegwidden welcomes Harm back to JAG by assigning him a tricky case - defending the son of the Secretary of Navy. Harm takes the case when Lt. Nelson, the son of the Secretary of the Navy, is accused by Cmdr. Burke of disobeying an order at sea, an act worthy of a court martial.

The key eyewitness in an attempted rape trial, a decorated Marine corporal, suddenly goes AWOL after he is asked to testify. Harm and Bud follow his trail, and they begin to uncover disturbing facts about the corporal's past that explain why he needs to stay out of the limelight.

Trouble in the JAG office starts when Gunnery Sgt. Victor Galindez, ""Gunny,"" is charged with assault following an off-duty altercation outside a gay bar. It comes to light that P.O. Tiner was also involved in the brawl, having come to the aid of his companion, whom Gunny was roughing up.

Meanwhile, Mac finds herself wrestling with the ""don't ask, don't tell"" policy as attitudes toward Tiner change around the office under suspicions that he's gay.

When an inept seaman's apparent suicide aboard an aircraft carrier turns into a murder investigation, Harm and Bud try to find out what really happened.