Harm represents the divorced Marine colonel Anderson who has overextended his custody agreement when attempting to spend time with his son before his mother moves him far away. But a warrant goes out to for Anderson, on whom the Vietnam war left its marks. After a local deputy attempts to arrest him without success, a strong police force goes after him. Harm learns what Anderson is really up to and helps him to reach a lodge, the place where he promised to bury an old pal who died back in Vietnam, but was left behind. Locations: Vietnam (1972); California (Tustin, Santa Ana,Big Pine, Bishop)

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.

Annie Pendry, a widow, comes to Harm for help after her young son, Josh, witnessed a murder while on a class trip to Andrews Air Force Base. After Harm and Josh are the targets of a drive-by shooting, Harm moves Josh and Annie into his apartment -- and into his life. Harm discovers that the original crime and the drive-by shooting are tied to a ruthless international arms dealer, but not before Josh is kidnapped by the dealer in order to silence him as a witness.

When a luxury yacht owned by a reputed South American drug trafficker mysteriously sinks and the Navy is suspect, Harm, Mac and Bud are put on the case. Meanwhile, Artemus Sullivan, a World War II Navy veteran, with the help of his aged cronies, devises plans from a nursing home to make sure the drug dealer responsible for Sullivan's grandson's death is brought to justice. But when Sullivan is kidnapped by the drug dealers, his mettle is tested, as is that of Harm and his team as they race to rescue the war hero.

Mac's ""little sister"" unexpectantly shows up at JAG headquarters, declaring that she's run away from her abusive stepfather. While she investigates whether Chloe has been abused, Mac has her hands full keeping her from turning the office upside down, then learns that her real father is still alive serving on a ship in the Navy. Despite the cost, Mac convinces the Admiral to allow the two to talk to each other via satellite video-conferencing.

Meanwhile, Harm spends the evening interrogating a beautiful Navy doctor arrested for DWI after she lost control of her vehicle on icy roads and ran over a Nativity scene. Harm agrees to defend her when he learns that just before the accident and before she took the breathalyzer test, she had drank some liquid cold medicine (which contains 25% alcohol)

Adm. Chegwidden's attempts to fly to Italy to spend Christmas with his daughter, however, with the Washington, DC area mired in snow, most of the flights out have been cancelled.

When three U.N. peacekeepers are taken hostage in Kosovo, a SEAL team is sent in to rescue them before the end of a 24-hour deadline set by the terrorists. But when heavy ground fog delays the SEAL team by 30 minutes, the hostages are found dead and the team is blamed for their deaths. Mac and Bud begin to defend the team only to have Bud removed because of the defendants' lack of confidence in his legal expertise. Meanwhile, Admiral Chegwidden spends his vacation acting as technical advisor on a movie about the Navy and runs afoul of the Hollywood types who hired him.

When Navy SEAL Medal of Honor winner Lt. Curtis Rivers is fired upon while on a training mission, he returns fire only to discover that he has shot a seemingly unarmed 14-year-old boy. During Harm and Mac's investigation, they discover that the boy may have been accompanied by his uncle, a fugitive wanted by the F.B.I.

When Rivers goes AWOL to track down the fugitive and is captured by separatists, Harm and Mac find themselves not just investigating the case, but trying to defend Lt. Rivers in a court that does not recognize the U.S. government and its laws.

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.

When a Navy research project involving psychic phenomena goes awry and results in the death of one of its research subjects, Harm defends the admiral in charge of the project. As Mac prosecutes, she steadfastly proves that the admiral's ESP theories are wrong. But when her friend Chloe disappears and Mac experiences a vision that could save her life, she begins to have second thoughts about the paranormal.

When U.S. and Turkish ships collide during a NATO exercise, Harm and Mac defend the U.S. captain, who is being made the scapegoat for political reasons.