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Harm and Mac in Afghanistan, Chegwidden and Singer at the Pentagon, and Sturgis on the submarine Watertown are all working to uncover and stop an attack on the Seahawk carrier group.
Bud and Coates investigate a claim that a stray Navy bomb destroyed an Afghanistan school.
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 Qaeda 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.moreless
Harm defends one of JAG's most respected judges against Mac and Sturgis when he's charged with road rage and vehicular manslaughter. Webb learns that Kabir Atef is in Russia as part of a plot against U.S. military. He hooks up with Captain Volkonov searching for leads.
When the alleged architect of 9/11 is captured in Afghanistan, Harm and Mac prosecute against Chegwidden and Turner in a military tribunal.
When Harm and Mac are called in to investigate an aborted SEAL operation in Afghanistan, Harm accuses a television news reporter accompanying the SEALs for disobeying orders and causing the error. Meanwhile, Lt. Roberts receives his orders and, leaving Harriet and A.J. behind, ships out for a six-month deployment aboard the USS Seahawk.moreless
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.
Tensions run high at JAG when charges of negligence are brought against Bud for not defending his last client effectively. As Harm defends Bud, Sturgis prosecutes and Bud fears that Sturgis has damaging evidence against him. Just when Bud thinks things can't get any worse, Sturgis calls a surprise witness - Mac - who reluctantly takes the stand against her colleague.moreless
Harm and Mac return to the aircraft carrier USS Seahawk ("A New Life" & "Crossing the Line", among others) to brief the JAG officers on the new Rules of Engagement, following the escape of Taliban fighters as a result of a JAG officer's hesitation to determine if the target was legitimate.
While Harm is aboard the ship, the captain asks him to fly a bombing mission into Afghanistan. However, Harm's excitement changes to concern when his plane sustains critical damage from enemy fire.
Meanwhile, a jealous Lt. Singer sabotages Bud's case when she hears of his imminent promotion.
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.moreless
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.moreless
Mac's psychic vision talents come into play when a female Naval officer is found with her throat slashed in a local park. What originally seems like an open and shut case involving a love triangle that led to murder becomes much more when Mac's "visions" show her puzzling images that lead to evidence of an international conspiracy. Together with Sturgis Turner, Mac follows the clues to uncover information that leads them to a possible terrorist plot in Russia to steal nuclear weapons.moreless
It's Christmas, and Harm has to watch over a petty officer charged with larceny when there's nowhere else to take her.
Mikey Roberts is informed by Commander Lindsey that he's been nominated for an appointment to Annapolis.
Webb gives Harm an unexpected Christmas present.
Harm defends Lt. Barrett who readily claims he disobeyed orders and destroyed the EP-3 spy plane held hostage by the Chinese because he believed it was the right thing to do.
Harm and Sturgis go head to head at the lieutenant's court-martial as Harm tries to keep him out of Leavenworth, where he could be sentenced to 25 years for his actions.
Meanwhile, Mac investigates a charge of sexual harassment when a female officer charges a Marine colonel with humiliating her publicly when her training tape is shown on the television show "Military Bloopers." As part of her investigation, Mac takes the Colonel up on his offer to complete her regular physical training evaluation with the Colonel. Mac recommends that the Colonel get a letter of reprimand, which could jeopardize his chance for a command.
However, when it comes to light that it was the female officer herself that leaked her video to "Military Bloopers" in order to shift blame for her inability to pass the court, she is the one who finds herself in legal trouble with JAG.
A Navy P-3 spy plane is rammed by a Chinese MIG and is forced to land at a Chinese Air Base. (The second such incident; the first being the actual incident that occurred early 2001)
The SecNav requests Adm. Boone re-activated to active duty, in order to travel with Harm to the Air Base to negotiate with the Chinese for the release of the plane & crew.
Meanwhile, Mac, Bud, and Sturgis deal with two seamen from the Academy who engaged in a duel.
After the Chinese Commander is presented with photographic evidence that the MIG & its pilot that rammed the P-3 is alive & well (contrary to claims by the Chinese that the pilot was killed), the Chinese immediately release the P-3 crew; however, they would ship the P-3 back, piece by piece.
Lt. Barrett flying out to escort the plane from Chinese Air Space back to the USS Thomas Jefferson. After telling his wingman a lie to leave the escort, Lt. Barrett disobeys orders, flies into Chinese airspace & destroys the P-3 on the ground.
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.moreless
**November 2, 2001** Harm defends a Marine who says he was obeying verbal orders when his violation of the rules of engagement led six soldiers to their deaths in a ambush.
Harm faces disbarment for violating attorney-client privilege when, while defending an old friend from fraternization charges, he uncovers evidence of espionage and top-secret materials go missing.
Mac defends a lieutenant in a custody battle over a young girl whose father is accused of having broken her arm.
**August 15 - 17, 2001** After a break-in and murders at a Naval Annex building in Washington, D.C., Harm finds out that one of the victims was a friend of his, who is also suspected of passing information to the Chinese. As Harm sets out to clear his friend of espionage charges, he encounters startling roadblocks put in the way of his investigation by the intelligence community. Meanwhile, Renee shows up at JAG Headquarters with surprising news for Harm, and Mac tirelessly searches for the young girl she left behind in Indonesia. (See, "Guilt")moreless
"AUGUST 7, 2001" Following the transfer of a U.S. Marine accused of rape from the local Indonesian police to his CO at the Indonesian consulate, the consulate comes under siege by angry, armed locals. When the commander of the Marine detachment is killed and his next-in-command is blinded during the surprise attack, Mac realizes that she is next in command and must organize the emergency evacuation of the consulate under fire. Back at JAG, Harm defends a SEAL accused of killing a person onboard a flight that Harriet was a passenger.moreless
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.
Unwilling to face her pain over Mic & Harm, Mac is granted temporary assignment on the carrier USS Guadalcanal (along with Gunny) when the staff JAG there disappears.
Harm returns to active duty after returning from Renee's father's funeral.
*May 19, 2001* Harm's chance of being rescued from the Atlantic Ocean hinges on Mac's psychic ability (first seen in Season Five "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.moreless