When Harm is forced to shoot down a civilian plane flying in a ""no-fly"" zone in the Persian Gulf, Harm once again finds himself on the wrong side of the court-room.

Part of the JAG team goes to San Diego. Harm stays back as acting JAG. While he is there, a huge snowstorm strikes and Mattie is injured in an accident. Meanwhile, Mac and Vukovic find themselves working close to each other on a case at Camp Pendleton.

A marine Private kills a seemingly unarmed civilian in a raid on a Mosque in Karbala, Iraq. Lt. Vukovic goes to Iraq in order to defend the marine -- a hard task as the whole incident was filmed by a ZNN reporter. Meanwhile, Cresswell asks Mac to talk his daughter out of her plans to abandon a military career, and Harm maintains his vigil at Mattie's bedside.

Mac goes to Iraq to investigate a bombing that killed a group of Marine reservists, while Harm and Bud go to Oklahoma to assist their families, but end up prosecuting the sole survivor, who is accused of starting a fire that destroyed the Marine Reserve Center.

Gen. Cresswell's brother believes that remains found of a Vietnamese soldier are those of a helicopter pilot who saved his life during the war. Vukovic and Graves end up going to South Vietnam in search of a relative of the man's for a a DNA match.

Harm and Vukovic are teamed up to defend a sailor accused of manslaughter. Bud is assigned to prosecute what soon becomes dubbed "the dream team." At the end of episode it seems that Harm and Vukovic hold the ace but Bud has a surprise for them. General Cresswell then informs Mac that she is being posted to San Diego and Harm that he is being posted to London.

General Cresswell informs Harm and Mac that they are being reassigned. Harm to London and Mac to San Diego. With their deadline quickly approaching. Harm and Mac must sort out their lives and resolve their feelings for each other.