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.

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 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.

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.

When a Marine colonel defies orders from superiors, as well as the State Department, and rescues his men who are being held and tortured by a Haitian warlord, he is court-martialed. Harm and Mac are assigned as prosecutors and are shocked when they find they must go head-to-head with Chegwidden.

Bud was put in a position to choose which side to go on. He choosed Admiral Chegwidden

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.

Clark Palmer, a renegade government agent, breaks into Harm's apartment and incapacitates him. Palmer then makes a cast of Harm's face in order to prepare a mask that he can wear to pass for Harm. Palmer plans to murder the key witness in the trial at which Harm and Mac are currently prosecutors.

When Harm doesn't show up for the start of the trial, Mac takes his place, leaving Bud to search for the missing JAG lawyer. When Bud finds Harm trapped in an ingeniously booby-trapped apartment, the two must find a way to escape before the assassin can carry out his plan.

Members of the JAG team encounter resistance from Navajo tribal elders when they insist on DNA testing to verify that human remains are those of heroic Navajo ""code-talker"" Jimmy Blackhorse, who has been missing since World War II. Forensic pathologist Lt. Cmdr. Teresa Coulter joins Harm and Mac on the case.

The Navajo elders consider it a sacrilege to tamper with the remains of the dead and, furthermore, the Navajo medicine woman is certain that the remains do not belong to the esteemed Blackhorse. While the veracity of scientific evidence is argued against that of tribal custom and the metaphysical, Teresa finds herself falling for Harm and putting the entire assignment in jeopardy.

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.

Harm and Mac use a party at the Sudanese Embassy as a cover for their investigation of a kidnapping, and they're literally caught by surprise when terrorists take the visiting dignitaries -- and Mac -- hostage.

Meanwhile, Bud notices that Harriet seems to be suffering from more than just flu symptoms.

After Admiral Chegwiddens daughter, Francesca, is kidnapped in Italy, Chegwidden meets with his ex-wife, Marcella, and her husband, a wealthy Italian businessman, to get more background on Francesca's friends -- and enemies. Chegwidden learns that Francesca was seriously involved with the heir to a Mafia family -- a man Harm and Mac believe is responsible for the theft of Navy missiles for sale to Afghanistan. All intelligence points to the fact that Francesca is caught in the middle of this business deal gone awry, and it's up to Chegwidden and Harm to rescue her from the mob.

Millions of viewers are turned into witnesses when they see a Marine guard shoot an arrested terrorist on live television, and its Harms job to defend him. With Mac on the prosecution, she and Harm are pitted against each other in what seems like an open and shut case of cold-blooded murder. But when Harm is replaced by a civilian attorney with a defense plan that doesnt add up and whose fees are being paid by a wealthy right wing industrialist, Percival Bertram. Harm decides to do some investigating of his own.

Harm and Mac find themselves too close for comfort when they are sent to investigate an international incident on a nuclear submarine.

When Harm and Mac, who are already getting on each other's nerves, find themselves in the cramped quarters of the submarine, their relationship is stretched to the absolute limit. Their attempts to stay out of each other's way as much as possible are futile since they must work together to find out why the sub surfaced miles off course, sinking a Norwegian boat in the middle of a regatta.

Initially, it seems that the incident was the result of reduced staffing due to a breakout of E-coli. However, as more health problems begin to arise aboard the sub, Harm and Mac suspect a more criminal element than disease.

Numerous power outages & a ruptured steam line injuring a sailor sends Mac & Harm to the aircraft carrier USS CORAL SEA. While there, they discover two civilian technical representatives onboard and their plan to steal over a million dollars in cash from the Disbursement Office vault; as well as their plan to smuggle it off the carrier. Adm. Chegwiggen helps a former juvenile delinquent who became a decorated SEAL face his leukemia.

Harm fears he's losing his mind when he begins to see and hear his deceased father. Worried that he may be going insane, Harm finally confers with his Navy psychiatrist girlfriend who tells him she's treating a Marine officer with similar symptoms and suggests that Harm isn't experiencing anything unusual for someone who's lost a loved one under stressful circumstances. But before Harm can come to terms with the visitations, he begins to suspect that there's something more sinister involved that could cost him more than just his sanity.

With Harm's eyesight fixed, Harm decides to go ahead and submit a request to be transferred to a fighter squadron. When Lt.Cmdr Parker finds his written request, she is upset at the prospect of Harm being gone for months at a time.

Afterwards, Harm goes over to Mac's apartment who has Chloe spending the night with Mac before she is reunited with her real father. Harm informs Mac of the eye surgery and his plans. Mac is equally upset at the prospect of losing Harm. Mic shows up at Mac's apartment after Harm leaves attempting to court Mac's feelings. After Mic leaves, Chloe tells Mac that Brumby and Harm have a crush on her and begins teasing Mac: ""Harm & Mac, sitting in a tree, k-i-s-s-i-n-g.""

Admiral Chegwidden passes Harm's request to be transferred onto the SecNav. Not willing to do any favors for Harm, the SecNav is reluctant to intervene.

While patrolling the Mediterranean near Yugoslavia and against the orders of Harm, his division commander, Lt. Buxton fires on what he believes is a Serbian armored car about to attack Kosovar refugees. As Buxton and his pals are celebrating his victory back aboard the aircraft carrier, however, the grave news arrives: those ""Serbs"" Buxton attacked and killed were, in fact, Russian peacekeepers, and Buxton made the mistake while under Harm's command.

Mac prosecutes what appears to be an open-and-shut case of a Marine weapons expert accused of reckless endangerment.

Harms fitness report is coming up and the realization that maybe it really is too late to be a fighter pilot.

During a dangerous mission over hostile Serbian territory, Harm's wingman's plane is shot up and Harm performs top-gun maneuvers to keep the disabled plane aloft until it's over friendly territory.

Meanwhile, with a new Gunny in the office, Bud & Tiner fall over themselves as they compete against each other in an online auction to purchase tickets to a concert, in order to impress the Admiral. They end up looking foolish when it is discovered that the Gunny got the same tickets for free.

Harm and Mac are sent to Panama to investigate the wife of a Marine officer, Olivia Dunston, suspected of smuggling drugs into the U.S. When faced with the evidence, Olivia feebly denies the allegations, leaving Mac thinking that she's guilty of the charges.

On Christmas Eve, Harm pays his annual visit to the Vietnam Memorial to honor his father who was shot down on Christmas Eve, 1969. At the memorial, Harm meets a beautiful, but mysterious woman, who claims to have known Harm, Sr. She used to be a singer in a traveling USO tour and she met Harm's father shortly before his fateful flight.

In an unusual casting twist, Harm stars as his father in this episode, and many familiar faces show up playing different roles.

When the captain of a U.S. Navy frigate rescues a young girl in Cuban waters and sets off the beginnings of an international incident, Harm and Bud's investigation leads them to Cuba and a meeting with Castro.

Mac is assigned to represent an Arab princess not only at an INS hearing but also before an Islamic court, when the woman elopes with a Naval Petty Officer who is accused of smuggling her into the United States.

When AJ talks to Dr. Walden about what happened to his car, she is appalled that AJ would accuse her son of impropriety & terminates their relationship. Danny Walden is quite smug to AJ that he had been able to break them up -- which will come to haunt him later. With his car still being held by the police, he is dismayed with driving a rental car.

Harriet goes into labor 4 weeks early and a seemingly positive childbirth turns sour when it is discovered that the baby's head is pressing against the umbilical cord cutting off blood supply to the baby and her doctor (Dr. Gettis) is nowhere to be found. As another doctor steps in, Harriet is wheeled to the operating room in an attempt to save the baby.