On board the aircraft carrier USS Coral Sea, Harm & Admiral Boone await the arrival of the transport plane to take them back to DC. Harm was onboard the carrier to review the new Atlantic Fleet JAG command structure, while Admiral Boone was onboard making a business representation to the CAG of the Coral Sea. Admiral Boone, reassigned when SecNav Nelson was replaced, tells Harm that he's retired for good.

Just before they board their aircraft, the CAG tells Adm. Boone he was impressed with his presentation, but when Harm goes to shake the CAG's hand goodbye, the CAG refuses to take his hand, brushing him aside. Harm is left wondering why the CAG, who he had never met, appears not to like him. They then exit to the flight deck in time to see their plane about to land. The landing however, doesn't occur, since their tailhook broke away & landed on the deck.

In yet another ""ripped from the headlines"" episode, Harm takes his turn on the bench in a 'friendly fire' incident, whereby British troops were killed after an American pilot accidently dropped his bomb ordnance on their location.

Mac is assigned to prosecute the pilot, but has to deal with Harm's repeated impartial rulings. Harm though has his own problems as the SecNav makes it crystal clear to him that a conviction is required to satisfy the British.

News reporter Bill O'Reilly is featured.

Cdr. Turner gets to hitch a ride on a submarine that is bound for the mideast when it has been discovered that a 10-kiloton nuclear warhead has turned up missing.

Having felt betrayed in the past by the present members of JAG, Commander Lindsey delivers his report to the SecNav critical of the Admiral & the rest of the staff at JAG.

While conducting a flight test, Harm ends up involved in a serious CIA mission, over North Korea.

In Iraq, a Marine recon platoon is surprised by a 10 year-old Iraqi unarmed civilian tending to his goats. Surprised at seeing the armed Marine, the boy runs off. Later the platoon is involved in a skirmish, resulting in two deaths and the Sergeant losing their radio. Unable to call in for transportation out of the desert, the platoon must end up walking many miles in the desert to safety. Once safe, it is learned that the firefight was the result of the boy returning to his village & notifying some of the local Iraqi resistance members, who immediately went out to engage the platoon.

Harm is shocked to find that his life is making another unplanned turn, when he is notified that he is fired from the CIA for being inadvertantly shown on the cable news network ZNN carrying a young girl after landing on the USS Seahawk. Unemployed once again, Harm takes up crop-dusting to pay the bills.

At JAG, Commander Carolyn Imes who once worked at HQ-JAG (when she was a Lt. Cmdr), is brought back to HQ from overseas duty to fill the vacancy created by the departure of Cmdr. Rabb. But its Bud & Mac who are shocked when they learn that their old colleague falsified documents and has been practicing law without passing the Bar Exam.

And Catherine Gale "shocks" Harm with the news that she is pregnant.

Sadik Fahd who held Mac & Webb captive in Paraguay at the end of last season, shows up in Washington, DC and Mac has to wonder what he's up to when he begins to contact her.

Harm temporarily loses his hearing when the car battery on his Corvette explodes while he was working on it.

Members of the "JAG" staff are "helped" along to discover their true inner feelings while celebrating Jennifer Coates promotion to Petty Officer 1st Class.

A Naval Academy sailing team (that includes Bud's younger brother Mikey) is fighting a squall during practice when a female sailor is swept overboard and drowned. The JAG staff investigate whether the Commander was negligent when he ordered his team to sail through the squall.

Harm looks into the crash of a F-14 Tomcat.