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.
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 funeral.
**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.
""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.
**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"")
**October 20, 2001**
While filling in at Patuxent River for pilots that have been deployed overseas, Harm learns his friend, Cmdr. Scott Webster is being charged with fraternization with his RIO. Harm is granted permission to search his clients computer for any communication with his RIO which could be used against him. Cmdr. Webster receives a call that his son has been arrested for speeding & freeing to elude. Cmdr. Webster leaves Harm alone at the house while he picks up his son. Going through the hard drive, Harm discovers information that he might be considering selling national secrets, but attorney-client privilege prevents Harm from disclosing that information and his client does not wish to discuss it.
**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.
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.
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.
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.
Harm defends Lt. Barrett who readily claims he disobeyed orders and destroyed the P-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 her 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.
When a pretty female petty officer is arrested by the MP's for impersonating a Salvation Army 'bell-ringing' Santa & pocketing the cash, Harm is assigned as her attorney. However, since she has a history of unauthorized absences, she is ordered to be held in custody. But with the holidays, the brig & pre-trial detention center are unavailable, she is estranged from her father, so she must spend the holiday with Harm or with Mac.
Cmdr. Ted Lindsey (as the SecNav's administrative assistant) notifies Bud's brother Mikey that each year, the SecNav nominates 170 enlisted personnel for admission to the Naval Academy and that Mikey is being considered for one of those nomination spots. Bud & Mikey's father, a retired Master Chief though is not at all thrilled with having another son becoming an officer and insures that everyone knows it.
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.
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 faces Mac in court when he defends a Navy medical corpsman accused of murdering a Marine sergeant during a training exercise.
When he finds himself serving on the jury, Bud, feeling like an expert, uses his knowledge of the law during deliberations to help the jurors question the facts of the case, but then discovers the hard way that sometimes things in the courtroom are not what they seem.
Cmdr. Turner goes to New London to assist in the deployment of the submarine USS San Antonio. Once there, he helps a young sailor keep his marriage together when his wife intends to file for divorce due to the deployment.
When its learned that Harm has two tickets to the Super Bowl, everyone in the JAG office jockey for position in an attempt to be selected to go with Harm to the game. However, it turns out the ""tickets"" to the game are not necessarily the best seats for ""watching"" the game.
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.
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.
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.
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.
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.
In 1944, in the midst of World War II, a disastrous explosion rocked the U.S. Navy's Port Chicago near San Francisco, killing more than 350 sailors, most of them African-Americans. Following the blast, a group of 50 sailors refused to return to work until changes were made to assure their safety. They were charged with mutiny and court martialed, but later their convictions were reversed. Now, a surviving sailor wants his record and those of all the other ""mutineers"" cleared. Asked to handle the investigation discreetly, Cmdr. Turner discovers that an injustice was done and goes head-to-head with Lt. Singer in the courtroom. Meanwhile, Harm goes house shopping with Lt. Sims.
US Special Forces capture Mustafa Atef, who is believed to be a very high ranking Al-Queda official instrumental in training the hijackers who attacked the World Trade Center & the Pentagon. As a result, the President convenes the first military tribunal in over 50 years. As none of the JAG staff is eager to defend the accused terrorist, Adm. Chegwidden takes it upon himself to defend him, with Cmdr. Turner volunteering to sit second-chair for the Admiral. Harm & Mac are assigned to prosecute.
The tribunal is held aboard the USS Seahawk, so with the senior JAG staff flying out to the carrier, Lt. Singer is placed in charge of JAG's Administration Staff, much to the dismay of Harriet and the others. Lt. Singer then takes over the Admiral's office, conducting a fire drill and generally making a nuisance of herself.
On board the carrier, the staff are reunited with Bud, who as fleet JAG is assigned to assist Harm & Mac.
Harm, Mac & the Admiral return to the office from the USS Seahawk after finishing up with the military tribunal. The office staff is very happy to see the Admiral back in charge, after having to deal with Lt. Singer while he was gone, with Harriet making sure the Admiral knows how ""happy"" they are.
Their joy is short-lived however, when they learn that respected Navy JAG Judge, Captain Sebring is charged with having causing an another vehicle off the road which injured the female driver & killing her 6-month old daughter. Harm is given the task of defending him, while Mac is ordered into the uncomfortable position of prosecuting him. Seeing Mac's dilemma, Cmdr. Turner offers to sit second-chair with her, so that she won't be alone.
Lt. Singer overhears Harm & Mac discussing Bud & Harriet and learns that Bud doesn't know Harriet has bought a house, while Bud hasn't told Harriet about PO Coates.
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.
Admiral Chegwidden, Lt. Singer & Cmdr. Turner move over to the Pentagon War Room to easily coordinate & share intelligence information on Kabir Atef's planned attack on the U.S.
When an Afghan school is destroyed in a bombing raid, Bud & PO2 Coates fly to the scene to survey the damage. Once there, he promises to the locals that the US will re-build the school.
Meanwhile, Harm & Mac are still in Afghanistan attempting to pick up Kabir's trail, still looking for the mysterious truck that disappeared during a raid. ("In Country"). They come under fire, but are unhurt. Once they repair the damage to the vehicle caused by the gunfire, they continue driving all night and find an abandoned truck that appears to be the one they're looking for. They find the driver dead of suspected origin. Continuing onto the next village, they find villagers in the same condition. A medical team is brought in and they determine that the villagers are suffering from radiation poisoning.