Harm and Meg investigate the theft of stolen missiles at the SEATAC Naval Base. While interrogating PO1 Quinn of the theft, a prison-break takes place and Lt. Austin is taken hostage. Contrary to the Major in charge, Lt. Rabb thinks that this is a well-planned breakout with a big goal. Locations: SEATAC Island Naval Base and surrounding areas

Cpls. Ednar and Anderson mistakenly cross the Iraqi border. Trying to escape an Iraqi patrol, Cpl. Ednar is killed and Cpl. Anderson is taken prisoner. The Iraqi government invite the United States to send advocates to defend the Marine who's facing the death penalty for espionage. Harm and Meg are assigned to travel to Iraq to act as his lawyers as well as attempt to free the Corporal with the help of an undercover agent called 'Scimitar'.

Harm meets with a Russian 'contact' in order to purchase documents that will prove his father was taken to Russia after being shot down in Vietnam. However, during the transaction, they are interrupted by a KGB agent, Col. Parlovsky who shoots & kills the Russian, then runs off as FBI agents show up, finding Harm over the body, with the gun & documents he wrestled away.

As the FBI wants to hold him for the murder of the Russian, Adm. Chegwiggen manages to have Harm transferred to a military brig, and court-martialed, much to the dismay of the FBI agents. CIA agent Clayton Webb, knowing that it was Parlovsky, not Harm that committed the shooting, arranges for Harm to escape from custody in hopes Parlovsky will contact Harm.

In the end, Parlovsky makes contact with Harm, but they both get away before Webb can catch them. Parlovsky tells Harm the documents were a fake and burns them. He then leaves, refusing to help clear Harm of the shooting.

Mac arrives at Harm's apartment and is surprised to see that he has forgotten she was coming over and that he is getting to leave with a firearm. Stalling him, she gets him to tell her the story 2 years ago of the murder of his then-girlfriend, Lt. Diane Schonke, an Academy classmate, after her ship, the USS Seahawk docked in Norfolk. When Harm shows Mac a picture of Diane, Mac is stunned to see that Diane looks just like her.

When Harm tells Mac that he believes he has finally figured out who the real murderer is (Agent Turque) and that he intends to confront him, she gets him to initially agree to take her with him. Harm however tricks her and drives off, leaving Mac behind standing in the rain. Desperate to find Harm before he does something he'll regret, Mac calls Bud to meet her at JAG. Bud was an Ensign on Diane's ship and was one of the people who found Diane's murdered body. Bud tries to help Mac fill in the gaps and helps Mac learn that Agent Turque isn't the murderer.

Harm and Mac must don their diplomatic hats when they're dispatched to Tokyo to represent an ensign accused of raping a young Japanese girl. Once the trial begins, the disparities between Japanese and American courtroom procedures put Harm at odds with the ensign's Japanese defense attorney, in turn putting US/Japanese relations at an all-time low.

When what began as the trial of an ensign turns into a trial of the United States Navy, Harm and Mac realize that in order to defend the ensign from life in a Japanese prison, they must actually solve the rape case on foreign soil.