Harm defends a Navy SEAL accused of disobeying orders when his return to a hostile area in Afghanistan to retrieve a wounded comrade results in the death of another officer. Complicating the issue is the dead officer's pregnant widow who is determined to have justice served even though the accused man was her husband's best friend. Meanwhile, Admiral Chegwidden is asked to resign when he's charged with slapping a high school student.

Harm defends a female pilot accused of sexual harassment by a member of her crew who claims she ruined his future in the military because he rebuffed her advances. Harm is skeptical of his client's denials of the charges, while his co-counsel, Lt. Cmdr. Manetti, is sympathetic, causing tension between the JAG lawyers. Prosecutors Mac and Sturgis seem to have an open and shut case with their star witness testifying until Harm throws them a curveball that throws the case wide open.

A CIA mission sends Harm & Beth O'Neil to Libya to pull an agent out of that country. But when the agent wants Harm to transport the entire family, Harm has to modify his mission while avoiding contact with the Libyan authorities. When that fails and their plane comes under attack, Harm & Beth must land on the only available landing strip...the U.S.S. Seahawk.

At JAG, a Marine is accused of being involved with the Al-Queda terrorist organization and Mac is assigned to defend him against the charge.

When civilians are killed in a bombing raid, an International Criminal Court charges the United States with war crimes and the SecNav is the one on trial representing the USA. The SecNav is defended by Harm, Mac & Bud who find they must also defend the United States decision for waging the war. At the end, the court finds the USA on the following charges: Crimes against humanity - Not Guilty War Crimes - Not Guilty Intentionally targeting non-combatants - Not Guilty Willful destruction of civilian property - Guilty.

The court orders the USA to provide reparations to the town of Tikifa in the amount of $20 million US dollars. The prosecutor mentions to the SecNav that he doesn't agree with the verdicts, but pleased the SecNav won't have to go to prison. In response, the SecNav states that the two countries have been friends for too long and they both go off to get a drink together.

The season finale finds cast members in a total state of change: Admiral Chegwidden reveals a surprising decision he has made; Mac is given some news about her health and Harm is faced with a personal loss.