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.

Mac and Harm defend a Marine corporal (Steve Petrarca) who's charged with desertion. He claims that anti-Semitism drove him to leave the Corps and join the Israeli army, where he was awarded for heroism.

Harm defends a Marine gunnery sergeant who killed his wife, but claims it was self defense while he refuses to let his son testify on his behalf. Meanwhile, the JAG team bids farewell to Lt. Singer who is departing for the USS Seahawk.

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 is ordered to defend a plane-maintenance officer who he believes is guilty of making an error that caused the death of an aviator. Meanwhile, Harriet unintentionally impedes Bud's rehab when she insists he rest at home.

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.

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.

Harm doesn't have much hope in his defense of a two-star general court-martialed for disobedience and reckless endangerment during a wargame. His job is made more complicated when, in a rare move, Mac is appointed as the judge.

The future of seven seamen hang in the balance due to Lt. Singer's recommendation of court martial for all of them following a mishap on the ship. However, Singer's career could also be doomed if the father of her unborn child is someone on the Seahawk, and it's Harm and Mac's job to find out who it is. The problem is, the career-oriented Singer isn't talking, so Harm enlists the help of Lt. Manetti to do some sneaky behind-the-scenes investigating in order discover the identity of the father.

Harm and Lt. Cmdr. Manetti travel to Naples, Italy when an Interpol officer believes someone aboard a US destroyer is a serial killer who has killed four women while on leave in European ports.

Mac remains onboard the USS Seahawk until a replacement for Lt. Singer is assigned. (See ""Notes"" below)

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.

Harm and Mac investigate a Marine general claims that a Navy doctor caused the death of his teenage daughter during routine surgery.

Meanwhile, Bud is so frustrated with the simple cases he's been given, he decides to investigate what appears to be an open and shut case and gets surprising results.

Mac is called in to minimize the damage after a Navy lieutenant blows the whistle regarding deficiencies in a top-secret Navy combat device. When she helps the lieutenant get released from the military, she is furious when she later discovers that he had stolen hi-tech secrets to use in his video-game company.

Meanwhile, Harm is threatened with a lawsuit by an elderly lady and her shady lawyer following a minor traffic accident.

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.

When Harm takes Admiral Chegwidden for a ride in a F-14 Tomcat, AJ must fight for survival after accidently being ejected into a heavily forested area, blanketed in a snowstorm.

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.

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 murdered JAG officer teams up the JAG staff with agents of the Naval Criminal Investigative Services (NCIS).

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.

A year ago, Sturgis was assigned to prosecute Bud against charges that Bud was derelict in his duties while representing his client in court. Now, Sturgis competency in handling a case is questioned and Sturgis must now rely on Bud to successfully defend him.

When the CIA learns that a drug lord is attempting to sell missiles to terrorists, Clayton Webb (re-assigned to South America in "Need to Know") is assigned to prevent the deal from going through. To help with his cover, Mac is sent from Washington to masquerade as Webb's pregnant wife.

In Paraguay, Mac & Webb continue their mission to thwart the drug lords & terrorists.

Harm continues to deal with his emotions where Mac is concerned. Worried about her, Harm turns to CIA Attorney Catherine Gale for help in determining Mac's location. However, Harm ends up helping Ms. Gale with a personal issue.

In the final episode of the series 8th year turns out to leave fans of the show with facing yet another long summer of anticipation & speculation. When word reaches Washington, DC that Webb & Mac are missing, Harm insists on leaving for S. America to search for them, even if it means resigning his commission.