During a maneuver, transposed digits lead to a fatal bombing of a unit's own men. This causes several seriously wounded and eventually one dead soldier. Lt. Rabb and Lt. Austin are assigned to investigate this case because the responsible man is none other than Jay Williams, the son of Gen. Williams. But it seems the case is clear since Jay confesses that this mistake was his fault. Locations: MCB Twenty-Nine Palms

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

Harm and Meg investigate the theft of stolen missiles at the SEATAC Naval Base. While interrogating PO1 Quinn of the theft, a prison-break takes place and Lt. Austin is taken hostage. Contrary to the Major in charge, Lt. Rabb thinks that this is a well-planned breakout with a big goal. Locations: SEATAC Island Naval Base and surrounding areas

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.

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

Harmon Rabb is promoted and his first assignment as Lt. Commander is to defend Capt. 'CAG' Boone in a court-martial. During a mission over Bosnia, one aircraft goes down due to a system malfunction. A Serbian helicopter shoots at the parachuting crew and, to protect them, the CAG shoots down the helicopter. Is CAG, indeed, defending the crew from a hostile helicopter, or is he acting out of revenge, violating a cease-fire, and risking a war? Locations: Bosnia; Naples, Italy; USS Seahawk/Adriatic Sea; Washington D.C.

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

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

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 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.

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 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.

Harm risks ending the career of his mentor, as well as their friendship, when he investigates a training accident that killed two civilians.

When an F-15 has a mid-air accident and the occupants are forced to eject, a mother and her child are killed on the ground by the falling debris. Mac is assigned to represent the pilot as Harm investigates the cause of the accident and the leader of the training mission, Capt. Hachausen, his former flight instructor and mentor. When Harm's probe reveals that the captain's been covering up problems with his eyesight and the pilot of the plane is covering up for the captain, Harm must decide whether to reveal his findings -- information that would certainly end his mentor's career.

International tensions mount as Harm, Mac and Bud board an aircraft carrier in the Sea of Japan to investigate the accidental shooting down of a North Korean civilian airline by Navy jets.

While negligence on the part of the Navy fliers is indicated, Harm and Mac uncover evidence of a spy aboard the carrier. Meanwhile, the threat of war becomes real when a U.S. salvage vessel is sent to the site to help with the investigation and two North Korean warships threaten to sink it if both U.S. ships don't leave the area immediately.

Harm meets with a Russian 'contact' in order to purchase documents that will prove his father was taken to Russia after being shot down in Vietnam. However, during the transaction, they are interrupted by a KGB agent, Col. Parlovsky who shoots & kills the Russian, then runs off as FBI agents show up, finding Harm over the body, with the gun & documents he wrestled away.

As the FBI wants to hold him for the murder of the Russian, Adm. Chegwiggen manages to have Harm transferred to a military brig, and court-martialed, much to the dismay of the FBI agents. CIA agent Clayton Webb, knowing that it was Parlovsky, not Harm that committed the shooting, arranges for Harm to escape from custody in hopes Parlovsky will contact Harm.

In the end, Parlovsky makes contact with Harm, but they both get away before Webb can catch them. Parlovsky tells Harm the documents were a fake and burns them. He then leaves, refusing to help clear Harm of the shooting.

Harm, Mac, and Bud investigate claims of sexual harassment aboard an aircraft carrier. Mac's boyfriend, Dalton Lowne, is the defendant's attorney, and Mac is shocked when she discovers that he has been copying information from her files.

In order to solve the case, and combat Lowne's dirty tricks, Harm enlists the aid of Congresswoman Bobbi Latham. Justice is served, though many people's lives are changes as the result of Lowne's tactics.

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.

Political pressures come into play after an F-14 pilot clips a ski helicopter during a NATO exercise over Italian airspace, killing six civilians. Harm and Mac are assigned to opposite sides in the case, but the Italian government wants to prosecute on its own.

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.

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.

Harm and Mac's original mission is to represent a Navy flier whose Stealth jet is thought to have crashed in Iran due to a mechanical failure. But when the pilot slips Harm a message indicating that the $80 million plane didn't crash and is hidden, the assignment becomes nearly impossible: get the pilot -- and the costly aircraft -- back to the U.S. without letting the Iranians know that the plane is intact.

When three U.N. peacekeepers are taken hostage in Kosovo, a SEAL team is sent in to rescue them before the end of a 24-hour deadline set by the terrorists. But when heavy ground fog delays the SEAL team by 30 minutes, the hostages are found dead and the team is blamed for their deaths. Mac and Bud begin to defend the team only to have Bud removed because of the defendants' lack of confidence in his legal expertise. Meanwhile, Admiral Chegwidden spends his vacation acting as technical advisor on a movie about the Navy and runs afoul of the Hollywood types who hired him.

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.

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.

Bud's underachieving brother is accused of making a mistake during a training exercise that nearly killed 15 Marines. But establishing his innocence proves to be a difficult task, thanks to the age-old tension between the Navy and the Marines.

Adm. Chegwidden frets over a speech he must give when he is to be given an award.

Mic Brumby returns unexpectantly to the States; Mac & everyone are stunned when he announces that he has resigned his Royal Australian Navy commission so that he could move to the USA and be by the "woman he loves."

Adm. Boone (CAG aboard the USS Seahawk, ""A New Life"" & ""Chains of Command"")is nominated to become the Sixth Fleet Commander. An anonymous informant accuses Adm. Boone of massacrering civilians during the Vietnam War, and Harm and Mac are given only four days to investigate the claim, in part one of a two-part episode.

Harm's former partner Kate Pike is considering transferring back to the JAG office. It becomes complicated when a former CO of Kate is being considered as the new Inspector General and Kate confides to Harm that he made unwanted sexual advances to her when she worked for him.

Lt. Singer appears at the door during Kate's conversation and soon afterward, the affair is reported by the Washington media, although Harm suspects Lt. Singer as the source, she denies she overheard anything.

Eventually, Kate decides that Washington is just not the place to work and decides to turn down the Admiral's job offer.

When U.S. and Turkish ships collide during a NATO exercise, Harm and Mac defend the U.S. captain, who is being made the scapegoat for political reasons.

Harm's friendship with Capt. Volkonov puts him in a precarious position when a Russian submarine blows up and the Russians claim that a U.S. submarine was responsible. It's up to Harm to convince his friend (& the world) that the accident was caused by a faulty new Russian torpedo, without divulging highly classified material.

Meanwhile, Mac is sent onboard the USS Watertown to observe when the Congressional committee headed by Rep. Latham investigates as to why women are not allowed to serve aboard submarines.

Renee & Mic are left behind wondering whether their really is something between Harm & Mac.

As Bud is defending his brother Mikey, a petty officer accused of murdering a Mexican in a barrom brawl, their father shows up.

Harm & Mac square off in court over a charge of illegal fraternization, but when they oral arguments become directed at each other & reflecting their own relationship, Judge Helfman recesses the court for the day with a strong admonishment to the both of them.

All the staff shows up at Admiral Chegwidden's house for Mic & Mac's engagement party. Lt. Singer shows up in a knock-out of a dress which stuns the Admiral for a moment, not used to seeing her in civilian clothes.

Bud shows up dress properly for once, but Harriet notices after arriving that he has peanut butter on his tie. Bud is mortified trying to get a tie from anyone, without much luck. Later, he is forced to remove his jacket when wine gets spilled all over him. Even more mortified, Bud feels desperately out-dressed.

Throughout the evening, Mac reminisces with the Admiral about past events involving the both of them.

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.

Harm's chance of being rescued from the Atlantic Ocean hinges on Mac's psychic ability (first seen in Season Five's "Psychic Warrior"). However, Mac is trying to cope with her conflicting emotions for both Harm & Mic. On the edge of going unconscious from severe hypothermia, Harm's fires several warning shots which attracts the rescue helicopter. Back onboard the USS Patrick Henry, Harm's vital signs start to fade out, but Skates words help him pull through. Transferred to Bethesda Hospital, Renee learns that Harm has partial amnesia and doesn't remember them being a couple over the past year. Mac's indecision about the wedding drives Brumby back to Australia. When Harm tells Mac on the phone to come to his place so that she doesn't have to be alone, she arrives only to learn that Renee has beaten her to Harm's place with the news that her father has died. Mac ends up in the rain with no one around.