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...
Bud has lost his right lower leg due to a mine in Afghanistan; during emergency surgery he faces bad trouble. Sturgis returns to Washington, and Harm and Mac disobey an order from the admiral. Bud encounters an astounding change of course.
A US Marine deserts his unit and joins the Israeli Army, then faces a trial in the USA. Bud returns from overseas, gets a Purple Heart and a warm welcome (from everyone except his father), then starts his rehab. Loren gets transfer orders.
A Marine stands accused of fatally shooting his wife. Mac prosecutes, and Harm defends. Bud and his father have trouble with Bud's condition, but each starts to cope. Nearly everyone gives Loren a happy farewell; Sergei returns to Russia.
A deputy sheriff dies while chasing a car carrying two SEALs in a Navy exercise. The driver stands trial for negligent homicide. Bud goes home, the new SecNav takes office, and Harm takes Meredith for a thrilling flight.
A RIO dies of hypoxia, traced to contaminated oxygen. Mac prosecutes the PO apparently at fault, Harm makes a poor defense, and Sturgis takes over. Harm runs into more trouble, but he finds the truth. Bud resents Harriet's protectiveness.
A woman CO gives bad marks on a fitrep of a man officer below her, and he accuses her of sexual harassment. Mac and Sturgis prosecute, Harm and Tracy defend, and Harm learns what the CO has hidden. Bud and the admiral have ups and downs.
A senator asks the new SecNav to obtain a declassification of the story of the loss of a nuclear submarine on a CIA operation in 1968 -- so that the families can finally learn about the loss of their loved ones. The senator is the daughter of the skipper of the boat. The SecNav turns to the JAG, who appoints a quiet and classified court of inquiry. Harm, Mac, and Sturgis serve as counsel to the court. Due to the extremely high classification of the mission, much wrangling takes place between the CIA and the Navy. However, a surprise piece of evidence leads Harm to the...
A general stands trial for alleged disobedience and reckless endangerment during a war game. Sturgis prosecutes, Harm defends, and Mac sits on the bench. A piece of evidence turns up at the 11th hour. Bud and Harriet hold a reception.
Loren seeks trials for several crewmembers after a mishap at sea. Loren is pregnant, and she refuses to name the father. Harm conducts a second investigation, and Mac replaces Loren. Tracy lends a hand; Meredith and Bud help each other.
In Naples, Italy, Harm and Tracy use criminal profiling to find the killer of four prostitutes murdered in Mediterranean liberty ports during visits by a certain US destroyer. Sturgis works with Bud, and Harriet tries to work with Loren.
Bud and Harriet hold a party on Christmas Eve in their new house for the JAG gang. Everyone runs into difficulties en route, but everything finally works out. Bud invokes, "God bless us everyone"; all agree and exchange, "Merry Christmas".