The episode starts with a short recap of where we left off last season: Bud & PO Coates walking along a dirt road enroute to attend the ground-breaking of the new school, when they spot a small boy playing in a field that had yet to be cleared of mines. As Coates runs for help, there is an explosion behind her. She turns in time to see Bud injured in the explosion and runs to his side. Coates insists that Bud must be transported on the helo that brought them in, that Bud won't be able to wait for the proper medevac chopper.

Bud is airlifted to a field hospital, critical, but still alive. As luck would have it, ZNN reporter Stuart Dunston just happens to be at the base camp when Bud is brought it. Dunston reports the arrival of an injured JAG officer that was brought it, but does not report the name. Chegwiggen advises Harriet, but reminds her he is still on the Seahawk. She tries to contact him by instant messaging, but does not receive a reply.

Harm prosecutes a sensitive case in an episode that sees the swearing in of a new Secretary of the Navy and the arrival of a new JAG Officer.

Shortly after assuming his new role, SecNav Sheffield appoints Lt. Cdr. Tracy Manetti, a Harvard Law grad, to Adm. Chegwidden's team. Her first assignment is second chair to Harm in a negligent-homicide case against Lt. Reynolds, a SEAL. While leading a guerrilla wargame among civilians in rural Virginia as a test of unconventional warfare, Reynolds failed to stop for local police, leading to a high-speed chase in which a deputy was killed.

Harm, Mac and Turner go up against the CIA's top counsel when the agency tries to keep a 1968 Navy sub tragedy, in which 129 men died, classified. In so doing, they must find a way around the CIA's classified information rules in order to follow the orders of the new Secretary of the Navy.

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.

A raid by agents of the Immigration & Naturalization Service (INS) on a boat carrying Vietnamese ladies being smuggled into the USA, also nets a distinguished Vietnam-native Marine Lieutenant, who is suspected to have a part in bringing the ladies in for profit.

Harm & Sturgis are assigned to see if the Lieutenants claim that he broke into the warehouse containers to steal is true, or if he really is one of the lead smugglers. They learn that when the Lieutenant was four years old living in Saigon with his mother, he was loaded onto the last helicopter evacuating people from the US Embassy in Saigon on April 29, 1975, just before the city was invaded by North Vietnam. As there was only room for 1 person left on the helicopter, his mother placed him onboard & stayed behind. He was then brought to the US & later joined the Marines, rapidly advancing through the ranks, becoming a pilot & earned great distinction for himself.

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.

A soldiers finds himself being investigated when his claim of killing an Iraqi prisoner makes the news.

During the all-star game of the Navy & Marine baseball players, a batter narrowly escapes being killed after being hit by a ball thrown at him by the pitcher. The pitcher then comes under scrutiny for possible assault charges.

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.

Cmdr. Turner defends himself against the complaint filed against him for displaying anti-Korean attitudes when assigned to deal with the SARS outbreak earlier.

Harm & Mac go up against one another in the case of a Marine General making public speeches stating Islam goes hand-in-hand with evil & terrorism.

Harm is asked to re-open a 20yr old case of a seaman accused of murdering a prostitute. He doesn't deny stabbing her but he didn't murder her. Harm finds out that a similar crime was committed and uses this to free the seaman who has been wrongfully imprisoned.

A Marine Colonel is on the President's short list to become the new Judge Advocate General sparking controversy while Harm & Mac investigate a Navy Ensign accused of shooting a Canadian fisherman.