Trouble in the JAG office starts when Gunnery Sgt. Victor Galindez, ""Gunny,"" is charged with assault following an off-duty altercation outside a gay bar. It comes to light that P.O. Tiner was also involved in the brawl, having come to the aid of his companion, whom Gunny was roughing up. Meanwhile, Mac finds herself wrestling with the ""don't ask, don't tell"" policy as attitudes toward Tiner change around the office under suspicions that he's gay.

When a former Vietnam POW arrives at JAG headquarters to report a murder he's just committed, Harm confronts a very complex individual who may know something about his MIA father. When Willie relates the fact that he was imprisoned with Harm's father and then blindsides Harm by claiming that his father was a turncoat, the information has a profound effect on the JAG lawyer. Willie, a very complex individual, has been waiting 30 years to tell his story in his own way. Ultimately, Harm finds out that Willie's murder victim was the contemptible, sadistic commander of the POW camp where Willie had been -- but that's just the beginning of Willie's incredibly sad war story.

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.

A top female helicopter pilot is accused of disobeying an order---to cease her affair with a married enlisted man, and a Congresswoman is determined to ensure the pilot's fair treatment as a potential court-martial looms.

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

Harm is called in to probe the death of Navy pilot Lt. Marion, son of US Senator Grace Marion, while training with the Navy SEALS. As he was there only for two days, it seems that the death was due to gross negligence. With the reports given by his superior and comrades, combined with the results of how how he died, it seems that the actual incident is a cover-up. Analyzing his equipment and learning that it was a combat mission (and not a training mission as stated), the facts then point at murder. The key to all this could be General Behnke. Locations: Washington D.C.; NAS Roosevelt Roads, Puerto Rico; Carribean Sea; Colombia

Harm represents the divorced Marine colonel Anderson who has overextended his custody agreement when attempting to spend time with his son before his mother moves him far away. But a warrant goes out to for Anderson, on whom the Vietnam war left its marks. After a local deputy attempts to arrest him without success, a strong police force goes after him. Harm learns what Anderson is really up to and helps him to reach a lodge, the place where he promised to bury an old pal who died back in Vietnam, but was left behind. Locations: Vietnam (1972); California (Tustin, Santa Ana,Big Pine, Bishop)

An evacuation training for a Space Shuttle team ends with a dead pilot caused by a broken cable. Harm and Meg investigate and soon determine that the cable was sabotaged. Harm's first suspect is promoted pilot Lt.Cdr. Lowry. As this is an important mission (repairing a spy satellite monitoring Southwest Asia) it can't be canceled. And since there isn't another eligible pilot, Lowry cannot be removed from the team. A training flight with Lowry and Harm on board has a fatal system malfunction - again sabotage. Lowrey can now be crossed out but the person responsible for these incidents must be found as the scheduled mission must proceed as planned. It is highly possible that there will be another 'unpleasant surprise' to stop this mission. Locations: AFB Vandenberg; Space

On a sailing trip near Hong Kong, Harm is captured by the Chinese military. They want him to reveal the United States' position in case the Chinese should take two islands (which are claimed by Taiwan) by force. To get this information, the Chinese employ various mind games including placing Harm's father in a adjacent cell. Cdr. Krennick and Lt. Austin are offered a deal which includes Harm's freedom and asylum for a Chinese military person. Locations: Hong Kong; Nantou, China

A killed Navy officer working at a destroyer's new defensive system is investigated by Harm with help from Lt. Pike and Cdr. Brockman. Later, during the testing of this system, a malfunction occurs and the system takes over the ship. Without any chance to navigate it, the ship drifts directly to North Korea where the North Korean Navy is already awaiting them. Meg, who came in later, tries with other technicians to break the lockout to regain control over the sabotaged system. Locations: Okinawa, Japan; Japanese Sea

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.

The convicted spy Jason Magida successfully escapes from Groton brig and his way leads him straight to Adm. Chegwidden, who was involved in his court-martial back then. Magida takes Chegwidden, Mac and Bud hostage. Claiming he was framed, he insists the three officers retry him. Harm, in between trying from outside to solve this situation with Webb's help, calls in a SWAT team and then has his hands full of keeping the team from killing Magida. Locations: Groton, Conn.; Falls Church

Harm and Mac face off on opposite sides of the courtroom at the trial of a Navy Seal accused of murdering his closest friend during a mission against terrorists. Despite evidence to the contrary and the accused's unwillingness to cooperate, Mac, who is defending him, feels there's more to the story than meets the eye. Her fervor causes Harm, who is prosecuting the case, to dig deeper into the dead boy's personal life. It is Harm who discovers that it isn't a case of murder -- but, in fact, the victim begged his friend to kill him in order to keep a secret from his father, a strict former Navy petty officer.

Harm and Mac investigate a female fighter pilot's charge of sexual harassment against her commanding officer. The pilot, Lt. Marilyn Isaaks, claims to have been grounded for pressing charges of sexual harassment against her commanding officer, Capt. Boone (guest star Terry O'Quinn). Capt. Boone claims he grounded her because she's a bad pilot. While Harm and Mac are called in to conduct a thorough investigation into the allegations, congressional intervention forces Boone to schedule Isaaks for a training flight -- an action that Harm feels will have deadly consequences.

Harm & Mac are sent to Belfast, Ireland when the child of Navy Lieutenant Nivens suddenly turns up missing and a note left behind indicates it was taken by Lorcan Barnes of the Irish Republican Army (IRA), who also happens to be the child's father. Arriving in Belfast, Harm & Mac are immediately at odds with the Royal Police, when they suggest ""negotiating"" with the IRA for return of the baby. Not finding much help, they go and search out the IRA on their own. Directed to a bar & told to ask for a particular type of beer. While playing darts, a man showing Mac the proper way to throw a dart whispers in her ear to go to an abandoned storefront. With the Royal Police tailing them, Harm and the baby's mother risk going to the storefront, while Mac boards a bus and leads the Police away from Harm.

The JAG team discovers an evil plot by a rogue CIA agent after two attempts are made on Admiral Chegwidden's life. After Harm and Mac uncover the fact that all the members of the admiral's former SEAL team have recently died under mysterious circumstances, the JAG team learns that Chegwidden and his team were part of a CIA-controlled SEAL mission during the Vietnam war. Suspecting that the murder attempts may be connected to the mission, they start an investigation that leads to the rogue agent's plot to eliminate all witnesses to a terrible incident that occurred during the mission. But when the assassin kills Chegwidden's girlfriend, he decides to take care of the job himself -- even if it means losing his stripes.

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.

Harm is assigned to escort a rambunctious and ravishing Romanian princess, whose life has been threatened if her father petitions to join NATO. Meanwhile, Bud wrestles with starting a romance with Ens. Harriet Sims.

A Colombian drug lord wants to deal for the life of a Marine who was left behind when the covert mission to kidnap him went awry.

Harm goes undercover as a Marine gunnery sergeant to help Mac in her investigation of questionable Marine training methods and becomes a victim of unsafe maneuvers himself. While undercover, Harm learns that the tough-as-nails officer in charge of Force Recon training, Capt. Koonan, introduces unexpected problems into the training missions as a means of teaching the men to react quickly to surprises during combat. In addition to testing the Marines' mettle, the method also doubles their chances of returning safely from combat. However, in the mission in which Harm is involved, the method backfires dramatically, leaving five men trapped in a training maneuver destined for a disaster that even Capt. Koonan can't reverse, and it's up to Harm to get the trainees -- and himself -- out safely.

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.

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.

Harm, Mac and Bud are assigned sea duty to be official observers during a joint war games exercise between U.S. and Russian naval forces, but the games take a deadly turn when the rival captains decide to make the battle real -- and Harm, Mac and Bud are trapped on board the warring ships. The captains are bitter enemies from Cold War days and have deemed this their final grudge match. Both are determined to make it a battle to the death, even if it means going down with their ships -- and taking everyone on board with them -- and it's up to Harm and Bud to defuse what could become World War III.

Harm and Mac find themselves courtroom adversaries when Mac is assigned to defend an admitted wife abuser whom Harm is prosecuting for the murder of his wife's boyfriend. Mac finds herself detesting the man whom she is supposed to be defending -- a man who reminds her all too well of her abusive father. Meaning well, Harm advises Mac that she's letting her personal feelings get in the way of her professional duties, but the advice enrages Mac and she takes out her anger on Harm as well as her client.