Harm and Mac investigate a supposed friendly-fire incident in Iraq in which a marine was killed by a member of the Iraqi Civil Defense Corps and both sides claim the other fired first.
The guards at Guantanamo Bay in Cuba are ordered to remove a detainee from his cell for interrogation. He resists, so the guards try to subdue him and end up putting him in a coma. It turns out the "detainee" was a disguised U.S. Army soldier and the whole thing was a training exercise. Harm is assigned to defend the guards while Mac argues that torture and excessive force are not appropriate even when dealing with terror suspects.
A friend from Coates' past shows up. She offers her friend a place to stay while she settles in. Another past associate shows up looking for her friend, soon he is killed. The police find some evidence linking Coates to the crime. Coates tries to find a way to clear her name.
Harm and Mac try to locate a Marine Captain, whose deserted and is leading native in a quest to hunt terrorists. Bud Sr asks his son for help when he receives orders to recalling him to duty.
Tension in the Persian Gulf runs high. A fishing boat nearly gets sunk by a patrolling helicopter when they grabbed mackerels that looked like weapons in the smoke. 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.
A sailor who has been tormented fights back against his tormentor, then his tormentor dies apparently from the fight. Bud prosecutes, and has to face off against Rabb and Vukovic. Harm becomes Mattie's legal guardian.
Harm is promoted to Captain, and assigned to London. Mac is assigned to San Diego. They start deciding which of the staff they want to take with them on their new assignments. Since they'll be half a world apart, it's finally time for them to face their feelings for one another. The end of the series.