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.

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.

Due to frustration at being unable to wrest custody of his son from his drug addicted wife, Corporal Wetzel was distracted during a war game exercise and crashed a tank. Accused of dereliction of duty, Wetzel admits to being diverted on the job, but insists that Mac and Harm must keep him out of jail, since his arrest would certainly mean losing his son.

Harm and Mac like Wetzel and understand that his frustration accounts for his poor judgment. But nobody's more surprised than they when Wetzel winds up in a tank in a stand-off with the military, questioning why he's being forced to choose between being a marine and being a father.

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.

Harm and Mac must don their diplomatic hats when they're dispatched to Tokyo to represent an ensign accused of raping a young Japanese girl. Once the trial begins, the disparities between Japanese and American courtroom procedures put Harm at odds with the ensign's Japanese defense attorney, in turn putting US/Japanese relations at an all-time low.

When what began as the trial of an ensign turns into a trial of the United States Navy, Harm and Mac realize that in order to defend the ensign from life in a Japanese prison, they must actually solve the rape case on foreign soil.

Harm volunteers to defend a psychotic Vietnam vet accused of aiding the suicide of a fellow V.A. patient. While Harm argues in court that Roscoe Martin withheld the victims medication as a way to free him from the trancelike state in which it left him, the prosecution claims that the lack of medication is exactly what caused the mans death. Disappointed with the direction of the case, Roscoe feels that the cards are stacked against him and engineers an escape from the V.A. facility with three other patients. Their escape takes them to Harms apartment, and a negotiable situation turns deadly when guns are drawn and a SWAT team swoops in to help with what it sees as a hostage situation.

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.

Word of her father's imminent death forces Mac to look back at the years of anger and resentment he caused her. She is furious that a priest is trying to convince her to forgive this abusive alcoholic, who was responsible for her own alcoholism. She comes to realize, however, that perhaps her anger had been misdirected all these years when her mother shows up -- after having abandoned Mac many years earlier.

Meanwhile, Harm takes a gamble and undergoes laser surgery as a possible cure for his night-blindness.

The key eyewitness in an attempted rape trial, a decorated Marine corporal, suddenly goes AWOL after he is asked to testify. Harm and Bud follow his trail, and they begin to uncover disturbing facts about the corporal's past that explain why he needs to stay out of the limelight.

Harm is trapped below deck on a sinking ship with a sailer, who has been accused of murder, and a guard. Some rescue equipment collapses, blocking the only escape route. As water begins to fill the room, the three men are certain that the situation is hopeless.

Mac goes undercover to help Harm investigate charges of sexual misconduct against Chief Petty Officer Merker who is the leader of the Wiccans, a local witches coven with many Navy members. The female seaman who brought the charges claims she was seduced when she fell under the man's spell, but Merker claims the sex was consensual. The Wiccan's attorney is sharp and claims his client is the unfortunate victim. However, Mac learns that another young woman suffered the same fate. He convinces her to testify and Merker is found guilty.

Later, Mac learns that Mic Brumby was also thrown into a compromising position while undercover in the Royal Australian Navy.

Harm reopens a 10-year-old murder case and unexpectedly incurs the wrath of the victim's daughter, his friend Lt. Cmdr. Teresa Coulter (Trisha Yearwood). Harm feels that the original trial attorney didn't dig deep enough into the case and as he pursues the investigation a new picture begins to develop.

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.

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.

Harm is stunned to learn that his former girlfriend, Lt. Cmdr. Jordan Parker has been found dead in her apartment, having been shot with her own gun.

Despite this evidence, Harm is unwilling to accept the premise that Jordan committed suicide & calls in Lt. Cmdr. Teresa Coulter to help examine the forensic evidence. Harm & Mac begin to look for possible suspects who would want to kill her, starting with her last boyfriend who had also been a patient of hers.

However, as each of the suspects are ruled out, they begin to look for other possibilities to explain her death. The investigation leads to a shocking discovery for Jordan's neighbor. Returning home, Harm is stunned to find a letter from Jordan in his mail. Jordan wrote & mailed it a few hours before she was killed; in which she tells Harm just how much she had valued their time together.

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.

**June 20, 2001** Still aboard the USS Guadalcanal, Mac is called upon to prosecute a Major accused of negligent homicide by the ship's Captain.

Much to Mac's surprise and dismay, Harm arrives on board to defend the Major and also try to clear the air with Mac regarding their relationship. But as they both become entrenched in the case in which the victim drowned during a nighttime exercise in extremely bad weather conditions, they're hard-pressed to find time to discuss their personal business. Meanwhile, Admiral Chegwidden has his hands full with his teenage goddaughter who has run away from home.

Personal rivalries surface in the JAG office when Mac assures Harm that she'll beat him to the finish line in the Jagathon for charity. Harm then sticks his foot in his mouth by giving Mac a six-minute head start in the race. Meanwhile, testosterone levels rise when Gunny and Tiner battle head to head to see who is in the best condition for the race. And, true to form, Lt. Singer starts a betting pool on who will finish the race last, leaving Lt. Roberts feeling crushed when he discovers that his co-workers favor him.

Harm defends a Navy SEAL accused of disobeying orders when his return to a hostile area in Afghanistan to retrieve a wounded comrade results in the death of another officer. Complicating the issue is the dead officer's pregnant widow who is determined to have justice served even though the accused man was her husband's best friend. Meanwhile, Admiral Chegwidden is asked to resign when he's charged with slapping a high school student.

Harm and Mac are sent to Saudi Arabia to defend a female U.S. Naval pilot who refuses to follow the local laws and wear traditional Saudi dress and veils. Lt. Joanne Donato's outspoken refusal to be escorted by males in public and to wear proper attire causes a strain on relations between a U.S. base commander and a local Muslim cleric. It also causes Mac to feel that the lieutenant is simply being a bad soldier and disobeying orders - that is until Mac is forced to abide by the policies herself. Meanwhile, Commander Turner and Rep. Bobbi Latham have a rocky first date, making the possibility of a second seem remote until Harriet and Bud come to the rescue.

Adm. Chegwidden agrees to help the White House with an event honoring Medal of Honor recipients, but only if he can investigate the case of a vet who was dropped from the list because of a shoplifting arrest. Meanwhile, Mac and Harm look into a fire aboard a destroyer.

Harm and Mac investigate a "collateral damage" incident in Afghanistan when an attack on an Al Queda terrorist kills three innocent civilians. With the help of forensic pathologist Cmdr. Teresa Coulter, Mac and Harm try to find out if any of the remains can be identified as belonging to Al Queda leaders. Meanwhile, when Harm and Mac lose control of their Humvee, they are thrown into a minefield where they're forced to spend the night together figuring out how to extricate themselves from the trap.

Mac and Harm defend a Marine corporal (Steve Petrarca) who's charged with desertion. He claims that anti-Semitism drove him to leave the Corps and join the Israeli army, where he was awarded for heroism.

On board the aircraft carrier USS Coral Sea, Harm & Admiral Boone await the arrival of the transport plane to take them back to DC. Harm was onboard the carrier to review the new Atlantic Fleet JAG command structure, while Admiral Boone was onboard making a business representation to the CAG of the Coral Sea. Admiral Boone, reassigned when SecNav Nelson was replaced, tells Harm that he's retired for good.

Just before they board their aircraft, the CAG tells Adm. Boone he was impressed with his presentation, but when Harm goes to shake the CAG's hand goodbye, the CAG refuses to take his hand, brushing him aside. Harm is left wondering why the CAG, who he had never met, appears not to like him. They then exit to the flight deck in time to see their plane about to land. The landing however, doesn't occur, since their tailhook broke away & landed on the deck.

When Harm takes Admiral Chegwidden for a ride in a F-14 Tomcat, AJ must fight for survival after accidently being ejected into a heavily forested area, blanketed in a snowstorm.

A year ago, Sturgis was assigned to prosecute Bud against charges that Bud was derelict in his duties while representing his client in court. Now, Sturgis competency in handling a case is questioned and Sturgis must now rely on Bud to successfully defend him.

When the CIA learns that a drug lord is attempting to sell missiles to terrorists, Clayton Webb (re-assigned to South America in "Need to Know") is assigned to prevent the deal from going through. To help with his cover, Mac is sent from Washington to masquerade as Webb's pregnant wife.

In Paraguay, Mac & Webb continue their mission to thwart the drug lords & terrorists.

Harm continues to deal with his emotions where Mac is concerned. Worried about her, Harm turns to CIA Attorney Catherine Gale for help in determining Mac's location. However, Harm ends up helping Ms. Gale with a personal issue.

Harm returns to Washington, DC and is shocked to discover that Admiral Chegwidden had actually processed his resignation through official channels. Also, a female petty officer listed as missing in action during Desert Storm is located in Iraq, married to a bedouin sheik. As a result, the Navy charges her with desertion.

Due to overloaded JAG caseload which was made worse by the review of all of Cmdr. Imes cases, the Admiral has the SecNav re-instate Harm's Naval Commission, clearing the way for Harm to return to JAG.

When a US submarine rescues 10 North Koreans after their vessel sinks in South Korean waters, Cmdr. Turner arrives from Washington to determine their purpose.

Mac learns to be careful what she asks for - as she is assigned to escort a female Marine prisoner, after having made the request that the prisoner should be escorted by someone able to control her.

The season finale finds cast members in a total state of change: Admiral Chegwidden reveals a surprising decision he has made; Mac is given some news about her health and Harm is faced with a personal loss.

A Naval Academy sailing team (that includes Bud's younger brother Mikey) is fighting a squall during practice when a female sailor is swept overboard and drowned. The JAG staff investigate whether the Commander was negligent when he ordered his team to sail through the squall.

It's Christmas Eve. Col. MacKenzie crashes her car on the way home, and while unconscious through a series of episode flashbacks and discussions with a base therapist deals with many of her issues including infertility, insomnia, loneliness, Webb, and Harm.