Adm. Boone (CAG aboard the USS Seahawk, ""A New Life"" & ""Chains of Command"")is nominated to become the Sixth Fleet Commander. An anonymous informant accuses Adm. Boone of massacrering civilians during the Vietnam War, and Harm and Mac are given only four days to investigate the claim, in part one of a two-part episode.

Harm & Mac defend Adm. Boone in court against the charges that he was responsible for massacrering civilians. Although he is eventually acquitted, he decides that it is probably best to retire from the service, despite Harm's objection that the Navy need men like him.

A Navy P-3 spy plane is rammed by a Chinese MIG and is forced to land at a Chinese Air Base. (The second such incident; the first being the actual incident that occurred early 2001)

The SecNav requests Adm. Boone re-activated to active duty, in order to travel with Harm to the Air Base to negotiate with the Chinese for the release of the plane & crew.

After the Chinese Commander is presented with photographic evidence that the MIG & its pilot that rammed the P-3 is alive & well (contrary to claims by the Chinese that the pilot was killed), the Chinese immediately release the P-3 crew; however, they would ship the P-3 back, piece by piece.

Lt. Barrett flying out to escort the plane from Chinese Air Space back to the USS Thomas Jefferson. After telling his wingman a lie to leave the escort, Lt. Barrett disobeys orders, flies into Chinese airspace & destroys the P-3 on the ground.

Harm defends Lt. Barrett who readily claims he disobeyed orders and destroyed the P-3 spy plane held hostage by the Chinese because he believed it was the right thing to do. Harm and Sturgis go head to head at the lieutenant's court-martial as Harm tries to keep him out of Leavenworth, where he could be sentenced to 25 years for his actions. Meanwhile, Mac investigates a charge of sexual harassment when a female officer charges a Marine colonel with humiliating her publicly when her training tape is shown on the television show "Military Bloopers." As part of her investigation, Mac takes the Colonel up on her offer to complete her regular physical training evaluation with the Colonel. Mac recommends that the Colonel get a letter of reprimand, which could jeopardize his chance for a command.

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.

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.