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.
Harm and Mac go to Saudi Arabia to defend Lieutenant Stephanie Donato, a female naval aviator who flies C-130 Hercules while serving with the U.S. Air Force, but refuses to wear the Abaya when off-base.
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.
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.
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 Radar Intercept Officer dies of hypoxia, traced to contaminated oxygen. Mac prosecutes the PO apparently at fault; Harm makes a poor defense and Sturgis takes over. Harm learns the truth eventually. 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.
As a favor from Congresswoman Lillian Dorning, SECNAV Sheffield asks the JAG staff to get the story of a submarine, USS Angel Shark (SSGN-559), which was lost on a CIA mission in 1968.
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".