Cpl. Parr shoots at an intruder, who he believes shot at him first, at the United States Embassy in Lima, Peru. The intruder, an unarmed 15-year-old teen, is killed. But he wasn't just any boy. He was the brother of Cpl. Parr's girlfriend who (according to her) is pregnant. Harm and Meg are tasked to determine if the teenager was, in fact, unarmed, or if this was an attempt to kill the ambassador. Locations: Lima, Peru

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

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)

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.

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.

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.

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 & Bud are sent to Twenty-nine Palms Marine Base to investigate the mid-air collision of 2 helicopters & subsequent crash of one helicopter which killed the pilot.

Upon arrival at the crash site, they learn that the ""other"" aircraft was not another helicopter as was first thought. A piece of wreckage that is found that belongs to the ""other"" aircraft only deepens the mystery. When members of the Defense Security Division appear onscene with orders to take over the investigation and crash site, Harm becomes convinced that a major cover-up is in the works.

The base commander, Col. Barrett gives Harm time to investigate further. When Harm & Bud are out driving the base at night, they see an unknown type aircraft flying above them and follows it, but are soon blocked by a fence over the road marking the property of the ""Bradenhurst Corporation"".

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.

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.

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.

When a fighter pilot claims he heard the voice of God tell him not to fire on an attacking Iraqi, Harm and Mac are sent in to investigate his claim. Despite the pilot's assertions that he heard God, Harm insists on finding a more ""military"" explanation. When Harm fails from the ground to discover the origination of the voice, he suggests that Rice duplicate his earlier mission to see what they can learn about the incident in the sky.

Mac's ""little sister"" unexpectantly shows up at JAG headquarters, declaring that she's run away from her abusive stepfather. While she investigates whether Chloe has been abused, Mac has her hands full keeping her from turning the office upside down, then learns that her real father is still alive serving on a ship in the Navy. Despite the cost, Mac convinces the Admiral to allow the two to talk to each other via satellite video-conferencing.

Meanwhile, Harm spends the evening interrogating a beautiful Navy doctor arrested for DWI after she lost control of her vehicle on icy roads and ran over a Nativity scene. Harm agrees to defend her when he learns that just before the accident and before she took the breathalyzer test, she had drank some liquid cold medicine (which contains 25% alcohol)

Adm. Chegwidden's attempts to fly to Italy to spend Christmas with his daughter, however, with the Washington, DC area mired in snow, most of the flights out have been cancelled.

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.

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.

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.