A rescue helo has picked up Skates, but Harm remains adrift in the sea. With Mac's uncanny help, a Viking finds Harm's life-raft, then a helicopter finds Harm, but his condition is critical. Mac declines to set another date, then Mic returns to Oz.
Mac postpones her wedding indefinitely, and Mic returns to Oz. Mac seeks TAD out of town, so the admiral sends her and Gunny to investigate the disappearance of a Marine major from a ship in the Indian Ocean. Harm heals and gives a ride.
The admiral helps to solve a problem for an unexpected visitor. In the Indian Ocean, Mac and Gunny investigate a death; Mac prosecutes, and Harm shows up, defends, and figures it out. Friction heats up between Harm and a civilian attorney.
In Indonesia a girl complains of rape by a Marine who protects a consulate. The police seize him, and Mac flies in; she functions as a lawyer and a Marine. An angry mob besieges the consulate. Harm and Loren defend a SEAL for a heroic act.
An intruder shoots three Navy people, killing two. One of the dead is a friend of Harm, who protects his reputation. Webb, counter-espionage, and disinformation are involved; Bud solves it. Mac and Renee return to town; Mac leaves again.
Harm defends an old friend against improper fraternization; while investigating, he finds something affecting national security, then he too faces serious questions. Mac helps a woman Naval officer with a case involving child abuse.
During a UN peacekeeping campaign a Marine captain, exceeding written rules of engagement, orders his team into an ambush, which kills six Marines. Sturgis prosecutes, and Harm and Bud defend. Mac investigates an unlikely peeping tom.
The JAG gang take part in a JAGathon, a charity-benefit marathon, which provides opportunities for personal pride and individual competitiveness. Sturgis feels uncertain, and Harm defends a sailor for impersonating an officer.
A Chinese MiG collides with an EP-3 Orion aircraft on a recon mission; the Orion lands at a Chinese airfield. Harm and RAdm. Boone go to China; they reclaim the crew but not the bird. An escort pilot takes matters into his own hands.
Harm, RAdm. Boone, and the Orion crew arrive aboard the carrier, as does the rogue pilot, who then faces a court-martial. Harm and Bud defend him. Mac passes a test, and she investigates demeaning behavior toward a woman Marine officer.
Amid much activity at Christmas, a woman petty officer in disguise runs afoul of the law, Harm takes her into custody and to a party, and she stays with Mac. Harm's rebuilt Corvette briefly disappears, and Webb gives him a surprise.
A woman Naval officer fails to keep an appointment with Mac and Sturgis; they search for her, then find her body. A suspect points them to smuggled uranium and a rogue terrorist group. Harm investigates a mishap at sea; Sergei meets Loren.
A teenage boy spits at the admiral, who slaps him on tape, and an uproar follows; however, the false denials and other lies of the boy overtake him. Harm defends a SEAL officer who disobeys orders by going back to recover a fallen mate.
A Navy hospital corpsman goes on trial for the murder of a Marine during a field exercise; Mac prosecutes, Harm defends, and Bud serves and argues on the jury but later has second thoughts. Sturgis helps a submarine family stay together.
At a US base in Saudi Arabia, Harm and Mac defend a woman Naval aviator who is assigned to a unit of the US Air Force, and who has disobeyed standing orders about the public off-base behavior of US women, including the wearing of abayas. The pilot in question, a native of Brooklyn, freely and vigorously expresses her views about such rules. With the support of the men in the same unit, Harm and Mac do their part in producing a positive and constructive conclusion. Meanwhile Sturgis and Bobbi have their second date, even after a rocky first one, and Bud and Harriet go ...
Harm and Mac go to sea during wartime operations. Harm flies the next mission, hits the target, and draws enemy fire; his aircraft sustains damage, but he safely returns. Bud runs into trouble at work, and Sturgis becomes closer to Bobbi.
The admiral orders a hearing about the allegedly inadequate defense by Bud in the previous episode. Sturgis prosecutes, and Harm defends. Harm discovers why Bud did not find a key witness and an alibi. The admiral meets an intriguing lady.
A fire breaks out in the galley aboard a destroyer at sea; personal injuries and materiel damage result. Harm and Mac investigate. The fire may have resulted from one or more human mistakes or maybe from the age of the ship, which is the second oldest destroyer in the Navy. A hearing takes place; Mac prosecutes a sailor who has confessed to a risky act, and Harm defends him. The admiral feels and shows much interest in an aging Marine who received the Medal of Honor for gallantry during the battle for Guadalcanal in WW2, but who has recently run into some trouble. Bud...
Harm and Mac prosecute a civilian reporter for disobeying a direct order while accompanying a SEAL team on a mission against a target in Afghanistan, and Sturgis defends. Bud carries out transfer orders to a ship as his next duty station.
A retired chief petty officer seeks a new trial about his involvement in an alleged mutiny after a disastrous explosion in 1944. Loren prosecutes, and Sturgis defends. Sturgis's father takes part. Harriet buys a house without telling Bud.
By order of the PotUS a military tribunal takes place aboard a ship at sea. The defendant is a top member of the Al Qaeda. Harm and Mac prosecute, and the admiral and Sturgis defend. Loren, as the senior officer, runs the place her own way.
A Navy judge stands accused of vehicular homicide. Mac and Sturgis prosecute; Harm defends. Harm discovers the real cause of the wreck. Webb continues to pursue a terrorist, and Loren continues to promote trouble between Bud and Harriet.
Harm and Mac in Afghanistan investigate a failed air strike against a leader of the Al Qaeda, and they encounter problems. Bud at sea successfully interrogates a suspect by using Star Trek concepts. Harriet makes an impression on Loren.
Al Qaeda has bought an old diesel-electric submarine from Iran, has recruited a Russian submarine captain and several Russian submarine sailors, and has loaded a submarine-launched cruise missile with a dirty nuclear warhead. The admiral, Sturgis, and Loren brief a three-star admiral in one of the war rooms of the National Military-command Center at the Pentagon. Harm and Mac, still in Afghanistan, follow the trail of the uranium, and they arrive aboard USS Seahawk (CVN-65) for testing for possible exposure to radiation. Sturgis goes as an adviser aboard USS Watertown...