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.

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.

(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.

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.

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.

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.

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.

Harm faces Mac in court when he defends a Navy medical corpsman accused of murdering a Marine sergeant during a training exercise. When he finds himself serving on the jury, Bud, feeling like an expert, uses his knowledge of the law during deliberations to help the jurors question the facts of the case, but then discovers the hard way that sometimes things in the courtroom are not what they seem. Cmdr. Turner goes to New London to assist in the deployment of the submarine USS San Antonio. Once there, he helps a young sailor keep his marriage together when his wife intends to file for divorce due to the deployment. When its learned that Harm has two tickets to the Super Bowl, everyone in the JAG office jockey for position in an attempt to be selected to go with Harm to the game. However, it turns out the ""tickets"" to the game are not necessarily the best seats for ""watching"" the game.

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

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.

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.

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.

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.

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 CIA mission sends Harm & Beth O'Neil to Libya to pull an agent out of that country. But when the agent wants Harm to transport the entire family, Harm has to modify his mission while avoiding contact with the Libyan authorities. When that fails and their plane comes under attack, Harm & Beth must land on the only available landing strip...the U.S.S. Seahawk. At JAG, a Marine is accused of being involved with the Al-Queda terrorist organization and Mac is assigned to defend him against the charge.

Harm attempts to gain legal guardianship Mattie, but finds his past single ""lifestyle"" may pose a problem in making good on his promise to her.

Mac is unable to accept the news that Clayton Webb really is dead and ends up in possible danger looking into Webb's "death". With the retirement of Rear Admiral A.J. Chegwidden, Cmdr. Sturgis Turner is named Acting Judge Advocate General.

When a female F-14 Tomcat RIO (Radar Intercept Officer) goes missing from the aircraft carrier U.S.S. Seahawk while stationed in the Adriatic Sea, the Judge Advocate General of the Navy, Rear Admiral Al Brovo (Kevin Dunn), sends young Lieutenant Harmon Rabb with Lieutenant Junior Grade Caitlin Pike on Bastille Day 1995 out to the carrier where they must find out whether her death was accidental or intentional.

Meg goes under cover as a Marine recruit in order to investigate the mysterious death of a female private in a boot camp. The facts point at the two drill instructors SSgt. Carrington and Sgt. Gonzales. But a newspaper clipping found by Lt. Austin changes the situation completely. Locations: Parris Island; Washington D.C.