Webb and Mac are prisoners of a dealer in Paraguay, where the bad guys torture Webb. Harm goes there to rescue Mac. Gunny tails Harm, they meet, and they attack. Gunny drives Webb to a hospital, and Harm and Mac destroy stored missiles.

With Mac undercover and out-of-touch, Harm turns to CIA attorney Catherine Gale (from "Need to Know") for help. Harm also plays along when she asks him to pose as her boyfriend in front of Gale's mother who is dying of heart failure.

Harm returns. Bud does poorly in representing Sturgis, who stands accused of giving inadequate counsel. The admiral tries hard to propose to Meredith. Mac poses as Webb's pregnant wife while undercover for the CIA in Paraguay. 

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.

A Boy Scout finds the decomposing body of Lt. Loren Singer in a tree. The NCIS investigates, and Harm becomes the prime suspect. The NCIS finds not only surprises about the death but also circumstantial evidence pointing straight to Harm.

A Navy hero returns from Uzbekistan and faces charges of a fraudulent enlistment because he is a man previously thought to have died on 9/11. The SecNav receives a rebuttal from RAdm. Chegwidden, then fires Cdr. Lindsey and throws him out.

The admiral returns. A Marine pilot and his wife become suspected of taking part in human trafficking. Harm and PO Coates find the truth, and justice prevails. The SecNav sends Cdr. Ted Lindsey to investigate the office; Ted grinds his ax.

Sturgis finds a missing nuclear torpedo; Harm finds missing cash and figures out a framing and other irregularities in a disbursing office aboard a carrier. The admiral continues to recover, and he names his new dog. Sarah runs the shop.

When Harm takes Admiral Chegwidden for a ride in a F-14 Tomcat, AJ must fight for survival after accidentally being ejected into a heavily forested area, blanketed in a snowstorm.

A Navy pilot drops a bomb on a British position, killing three soldiers and injuring others. In a court-martial he faces charges of involuntary homicide and dereliction of duty. Mac and Bud prosecute, Sturgis defends, and Harm presides.

A tribute to the Nurse Corps of the US Navy, especially in WW2, showing a fictional tale aboard a hospital ship offshore during the Battle of Iwo Jima. The regular JAG characters transition into other roles. An elderly man tells his story.

A Navy lieutenant ostensibly blows a whistle on an allegedly defective high-tech combat system; Mac helps him to resign, but she discovers his dishonest plot, and she helps justice to prevail. Harm meets a little old lady by accident.

A general demands to know why his daughter died during surgery, then he stands accused of improperly influencing the testimony of a witness. Harm prosecutes, Mac defends, and Mac finds the real cause of the death. Bud receives a welcome letter.

Christmas Eve events conspire to prevent the JAG team from spending Christmas Day together at Bud and Harriet's.

Harm works with Italian authorities to track down a serial killer that Interpol believes is a U.S. seaman.

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.

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.

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 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 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 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 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 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.

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.