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.
An Israeli soldier is charged with desertion - by the U.S. Marine Corps. Bud returns to the U.S. to begin his rehabilitation. Admiral Chegwidden admits to Harm that there is a major complication with his relationship with Meredith.
A Marine is charged with murdering his wife, but it is a lot more complicated than anyone realizes. Bud is having trouble getting started in his rehab. Lt. Singer gets her new billet - as JAG aboard the Seahawk. Sergei makes a big decision.
A deputy is killed in a car chase - but JAG gets involved when the "joyriders" turn out to be SEALs. A new SecNav gets sworn in, and a new lawyer comes to JAG. Bud comes home from the hospital. Harm takes Meridith up in his plane.
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 hugger who has killed four women while on leave in European ports.
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.
Harm and Mac investigate a Marine general claims that a Navy doctor caused the death of his teenage daughter during routine surgery.
Mac finds herself in a pickle when a Navy officer causes a media controversy by claiming a new high tech weapon is faulty. After being separated from the service, it surfaces that he created the flaw himself to exploit it for his own financial gain outside the service. Meanwhile Harm finds himself being sued by an old woman who he rear ends.
Set during the Battle of Iwo Jima in World War II, a Navy nurse falls in love with a wounded Marine.
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.
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.
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 cuddled 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 hug 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.
In Paraguay, Mac & Webb continue their mission to thwart the drug lords & terrorists.
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.