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.

Harm & Mac defend Adm. Boone in court against the charges that he was responsible for massacrering civilians. Although he is eventually acquitted, he decides that it is probably best to retire from the service, despite Harm's objection that the Navy need men like him.

Harm, Mac & the Admiral return to the office from the USS Seahawk after finishing up with the military tribunal. The office staff is very happy to see the Admiral back in charge, after having to deal with Lt. Singer while he was gone, with Harriet making sure the Admiral knows how ""happy"" they are.

Their joy is short-lived however, when they learn that respected Navy JAG Judge, Captain Sebring is charged with having causing an another vehicle off the road which injured the female driver & killing her 6-month old daughter. Harm is given the task of defending him, while Mac is ordered into the uncomfortable position of prosecuting him. Seeing Mac's dilemma, Cmdr. Turner offers to sit second-chair with her, so that she won't be alone.

Lt. Singer overhears Harm & Mac discussing Bud & Harriet and learns that Bud doesn't know Harriet has bought a house, while Bud hasn't told Harriet about PO Coates.