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.

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

A civilian tech rep aboard a submarine seizes control of an experimental torpedo after its launch during an exercise. The rep threatens to sink a cruise ship and demands a ransom. Harm and Ltjg. Meg Austin go to the sub and save the day.

During a simulated attack, a seriously wounded Marine is found on the beach. JAG is called in to investigate. Harm and Meg follow two ways: An executed Code Red or a brawl. Locations: Camp Pendleton and area; Los Angeles

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

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.

A murdered female lieutenant turns out to be Lt. Schonke, a friend with whom Harm attended Academy, but neither Cdr. Krennick nor Agent Turque, an abrasive civilian investigator, buys Harm's claim that his relationship was strictly platonic. After the primary suspect of the murder is also found dead - a more than dubious suicide - Harm finds himself being the number one suspect for both murders ... Locations: US Naval Base Norfolk, Va.; Washington D.C.

Harm teams up with Maj. Sarah MacKenzie and Lt. Roberts to investigate, together with Special Assistant Webb, the theft of the Declaration of Independence, which was stolen by Colonel O'Hara. O'Hara, who turns out to be Mac's uncle, claims he has taken control of it to remind the people - and especially the politicians - of its meaning and spirit. Locations: East of Yuma, Arizona; Red Rock Mesa; Washington, D.C.; Falls Church, Va.

Harm discovers evidence that his father, an MIA from the Vietnam War, may be alive and under KGB control in Russia.

Harm and Mac are investigating the murder of a Navy pilot whose body was found hidden aboard the decommissioned aircraft carrier the USS Hornet. With help from a local police lieutenant, they discover a motive for the crime, which involves a list of MIAs and POWs supposedly still alive and under KGB control in Russia -- and the list includes Harm's father. But before Harm can act on the information, the book mysteriously disappears along with the helpful police lieutenant.

Mac arrives at Harm's apartment and is surprised to see that he has forgotten she was coming over and that he is getting to leave with a firearm. Stalling him, she gets him to tell her the story 2 years ago of the murder of his then-girlfriend, Lt. Diane Schonke, an Academy classmate, after her ship, the USS Seahawk docked in Norfolk. When Harm shows Mac a picture of Diane, Mac is stunned to see that Diane looks just like her.

When Harm tells Mac that he believes he has finally figured out who the real murderer is (Agent Turque) and that he intends to confront him, she gets him to initially agree to take her with him. Harm however tricks her and drives off, leaving Mac behind standing in the rain. Desperate to find Harm before he does something he'll regret, Mac calls Bud to meet her at JAG. Bud was an Ensign on Diane's ship and was one of the people who found Diane's murdered body. Bud tries to help Mac fill in the gaps and helps Mac learn that Agent Turque isn't the murderer.

(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.

Having been shot at by Russian fighters, Mac & Harm are forced to eject from their plane, which then noses into the bottom of a very deep lake. The Russians announce to the world that Harm & Mac have been killed, which is broadcasted back to the USA by ZNN reporter Chuck DePalma.

Webb tries to convince the Admiral that they have been killed, but when A.J. learns their bodies haven't been found, A.J. becomes irate and vows to go to Moscow himself to look for them. The SecNav orders A.J. not to go, who replies that the SecNav doesn't want to try & stop him.

In Russia, A.J. meets with DePalma who tells A.J. that he doesn't believe the Russians, that certain things in their story don't add up.

In the woods, a husband & wife gypsies come across Harm & Mac. They are disappointed when they learn that Harm & Mac are not American Spies as at least the spies have gold coins to give to Russians that help them.

Admiral Chegwidden and Clayton Webb make an unlikely team when they join forces to save a C.I.A. agent from Italian terrorists. Webb already tried once unsuccessfully to liberate the C.I.A. agent, who was his mentor, and knows he needs backup in order to retry the mission. He approaches the Admiral, with whom he has a tenuous relationship, but who he knows credits the agent with saving his life in Vietnam. Together, Webb and Chegwidden go to Italy and put into motion a dangerous trap for the terrorists that, if it backfires, will kill all involved. Meanwhile, Harm suffers an identity crisis when his classic Corvette is stolen.

At the request of Lt. Cmdr. Brumby, Admiral Chegwidden sends Harm and Bud to Australia to represent a U.S. Naval officer, Kevin Lee, who has suddenly surfaced 28 years after being "murdered" by an Australian sailor. Lee contends that he accidentally killed his Australian nemesis years ago and, in a panic, exchanged identities with the dead man.

Now, charged with both deserting and murder, Lee is to be tried in an Australian court, pitting Harm against Brumby. Harm and Brumby are also about to go head-to-head outside the courtroom when Mac appears in Sydney and Brumby decides it's time to make her choose between him and Harm.

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

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.