General Cresswell informs Harm and Mac that they are being reassigned. Harm to London and Mac to San Diego. With their deadline quickly approaching. Harm and Mac must sort out their lives and resolve their feelings for each other.

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 and Mac defend a former Navy Seal, now a homeless man, but still a highly trained killing machine, who is accused of using excessive force in killing three men who tried to hold up a convenience store. It seems like an open-and-shut case of triple homicide until Harm and Mac discover that the former Seal, Paul Bauwer acted instinctively at the store as he sought to protect a young boy -- who happened to be his estranged son but didn't recognize him. Bauwer, embarrassed by his own vagrancy, wants to keep his identity a secret from his son. As a result, Harm and Mac must devise a successful defense without divulging their client's relationship to the only witness to the incident, while at the same time proving that Bauwer acted in an appropriate manner.

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.

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

The season finale finds cast members in a total state of change: Admiral Chegwidden reveals a surprising decision he has made; Mac is given some news about her health and Harm is faced with a personal loss.

Due to the transposition of two digits of a phone number, Lt. Austin receives a fax with the itinerary for a person with the codename 'Shepherd'. Later, a Commander from the Royal Navy shows up demanding that paper. After receiving it he shoots Meg, seriouly wounding her. Trying to find out who this 'Shepherd' is and why this document is so important, they end up chasing an assassin named 'Hemlock' apparently working for Russian hardliners and trying to kill the man behind 'Shepherd' - Boris Yeltsin who is due in the US for a secret treaty signing. Locations: Washington, D.C.; Bethesda; Leesburg, Va.

(The time is 1980, several Russian soldiers are guarding a prisoner who is Harmon Rabb, Sr. at a train station. The KGB take a photo of the persons gathered there - a photo which has made its way to Harmon Rabb, Jr. in the present time.) Clayton Webb meets with Harm at JAG and tells him who the men in the photo are. Webb mentions that one of them, Victor Lushov is now working in San Diego. Harm requests from the Admiral to take an F-14 hop to San Diego to visit his mother, keeping secret his true intentions. In San Diego, Harm meets with Lushov who turns out to be a Russian pilot who was instrumental interoggating Harm, Sr. after he was shot down over Vietnam, later befriending him. He tells Harm Jr. all about what happened to his father, that Harm Sr. fed all kinds of disinformation to the Russians, which was worse than telling them nothing. Lushov gives Harm Jr. the KGB file number for his father. And says he wants to live and will not repeat what he has said to anyone.

The murder/desertion trial of Kevin Lee takes a bad turn after his wife changes her testimony under cross examination. Harm and Mic fights to win over Mac

Mac becomes upset when Harm tells her at the last minute that he will not be attending her rehearsal duty in order to complete his 6-month required carrier landing qualifications. He assures her that he will be back in time for the wedding. At the church, Chloe is still wary of being friends of Mic. On board the USS Patrick Henry, Harm learns that the LSO who will be grading him thinks of him only as a "land-based Washington weenie." His fears that he won't be graded fairly are realized when he is ordered to land after his first attempt is waved off. After convincing the LSO that they were flying they way that the LSO taught them, he allows Harm to try again. After passing, he then completes his required night traps and requests to head back to Andrews AFB. With an approaching storm, all air operations are suspended, but is assured that he & Skates can be on the first Tomcat, once its forecasted to be safe. With a break in the storm, he & Skates are allowed to go.

When a pretty female petty officer is arrested by the MP's for impersonating a Salvation Army 'bell-ringing' Santa & pocketing the cash, Harm is assigned as her attorney. However, since she has a history of unauthorized absences, she is ordered to be held in custody. But with the holidays, the brig & pre-trial detention center are unavailable, she is estranged from her father, so she must spend the holiday with Harm or with Mac. Cmdr. Ted Lindsey (as the SecNav's administrative assistant) notifies Bud's brother Mikey that each year, the SecNav nominates 170 enlisted personnel for admission to the Naval Academy and that Mikey is being considered for one of those nomination spots. Bud & Mikey's father, a retired Master Chief though is not at all thrilled with having another son becoming an officer and insures that everyone knows it.

While searching for a girl who disappeared near an abandoned Naval Air Station, Harm and Meg watch the same mysterious lights and hear the same painful sound which also took place during Kathy's disappearance. Though it looks like alien movement, neither Austin nor Rabb believe in UFOs. While looking for the young girl on the base, they nearly get caught but thanks to Kathy they manage to escape, but are trapped on the base. Locations: Del Rio, Texas

After a lightning strike, a damaged Tomcat flying over Cuba is forced to land by the Cuban air force. Harm and Meg, accompanied by Cdr. Krennick and undersecretary of state Bair go to Cuba to negotiate the return of the pilot and aircraft. The main goal is to prevent the download of the Tomcat's classified software. But the CIA's actual plans are totally different ... Locations: Washington,D.C.; Cuba

GSgt. Crockett, instructor for snipers at the Boot Camp in Quantico, should be transferred to Bosnia. But there's a deal existing between him and his former commanding officers which says he won't be used in combat missions any longer. After shooting at the colonel 'to get his attention,' he is arrested. Since Crockett once saved Adm. Chegwidden's life, the Admiral orders an investigation to help him. But GSgt. Crockett escapes from the brig and hides in the mountains. Some marines, accompanied by Harm, go out to find Crockett, who's a well-trained and experienced sniper. Locations: Quantico, Va.; Washington D.C.

Hospitalized with a knee injury, Harm is forced to take action when the Hamas, a terrorist Islamic Resistance group, takes the hospital hostage. An Israeli diplomat undergoing a heart transplant provides the Hamas terrorists with the perfect negotiating tool. They take over the operating room -- as well as the entire hospital -- and use the diplomat as leverage while demanding the release of one of their imprisoned leaders. Meanwhile, Mac is trapped in the hospital cafeteria trying to negotiate with two terrorists.

Bud has his hands full when his obnoxious and abusive father, Big Bud, and his younger brother, Mikey, arrive in town for his wedding. Big Bud throws a stag party at a boisterous strip club where Harm's dress whites end up on the body of a stripper. A fight breaks out and Harm, Bud and Chegwidden find themselves in the slammer on the day of the wedding. While Mac goes downtown to bail them out, Harriet begins to have second thoughts about the imminent nuptials.

Lt. Elizabeth ""Skates"" Hawkes, Harm's former RIO (radio intercept officer), comes under fire after the crash landing of a Tomcat aboard the USS Patrick Henry. The ship's captain and Skates' commanding officer both place the entire blame of the crash on her shoulders and press for her court-martial. Barred from the initial investigation because of his relationship with Skates, Harm is finally able to help when he's called upon to defend his friend at her court-martial and employs all of his legal skills to save her military career.

Admiral Chegwidden, Lt. Singer & Cmdr. Turner move over to the Pentagon War Room to easily coordinate & share intelligence information on Kabir Atef's planned attack on the U.S. When an Afghan school is destroyed in a bombing raid, Bud & PO2 Coates fly to the scene to survey the damage. Once there, he promises to the locals that the US will re-build the school. Meanwhile, Harm & Mac are still in Afghanistan attempting to pick up Kabir's trail, still looking for the mysterious truck that disappeared during a raid. ("In Country"). They come under fire, but are unhurt. Once they repair the damage to the vehicle caused by the gunfire, they continue driving all night and find an abandoned truck that appears to be the one they're looking for. They find the driver dead of suspected origin. Continuing onto the next village, they find villagers in the same condition. A medical team is brought in and they determine that the villagers are suffering from radiation poisoning.

Harm & Kate continue to investigate the death of Lt. Angela Arutti, all the while the carrier remaining on combat status.

During a test flight Lt. Pendry has a deadly crash with his Tomcat. Harm and Meg are ordered to probe this case and the facts point to a pilot error, not at a system malfunction. Though Pendry was a risk-taking pilot, Harm doesn't think he has gone too far based on his knowledge from his flying days with Pendry. Locations: Miramar Naval Air Station; San Diego/area and off-coast

Harm and Mac play a deadly game of hide-and-seek in the Appalachian mountains when they are tracked by backwoodsmen poachers who have just killed a game warden. While on their day off, Harm takes Mac for a flight in his vintage airplane, only to be forced to make an emergency landing in a mountain clearing because of mechanical problems. While in search of help, they unwittingly surprise a band of poachers who have just murdered a game warden and who are now determined to kill Harm and Mac. Their lives in jeopardy, Harm and Mac must utilize every evasive military maneuver they've ever learned in order to escape the murderers who are now hunting them.

When a fully armed and piloted Navy F-14 disappears during a storm, the JAG team is called in to investigate all possible scenarios, from pilot suicide and terrorism to the curse of the Bermuda Triangle and UFO interference. When the plane's co-pilot surfaces, bloodied and disoriented, Harm and Mac get some new information that steers them away from Twilight Zone explanations and instead points them in the direction of kidnapping, terrorism and a hard-core militia group's plot to assassinate a PLO delegation heading for Washington by using the pilot -- and his plane -- to do the dirty work.

When a luxury yacht owned by a reputed South American drug trafficker mysteriously sinks and the Navy is suspect, Harm, Mac and Bud are put on the case. Meanwhile, Artemus Sullivan, a World War II Navy veteran, with the help of his aged cronies, devises plans from a nursing home to make sure the drug dealer responsible for Sullivan's grandson's death is brought to justice. But when Sullivan is kidnapped by the drug dealers, his mettle is tested, as is that of Harm and his team as they race to rescue the war hero.

When Harm and Mac set out to find C.I.A. Agent Clayton Webb's killer after his body is found aboard a burning ship, they inadvertently uncover a rogue government spy agency. Retracing Webb's steps, Harm and Mac learn that he was on a top-secret mission to deliver a high-tech weapons project to the proper authorities when he was stopped. Waiting for Harm and Mac when they discover this, though, is none other than Harm's former nemesis, ex-C.I.A. Agent Clark Palmer, now working with the rogue spy agency, who will stop at nothing -- including Harm's murder -- to get his hands on the top-secret project.

Unexpectedly, the wily Buxton demands that Harm and Brumby be his lawyers, thereby preventing Harm from testifying against him and forcing the two adversarial lawyers to work together. The contentious trial continues with Mac and Roberts prosecuting, and the pressure is enormous as the U.S. Navy and the Russian government vigilantly follow the trial to ensure that its own agendas are met. Meanwhile, the Navy has its own special plans for the troublesome Buxton.