A woman radar-intercept officer (RIO) disappears at night from an aircraft carrier in the Adriatic Sea. Two JAG lawyers, Lt. Harm Rabb and Lt. Caitlin Pike, investigate and solve. Harm, a former Naval aviator, unexpectedly becomes a hero.

The investigation continues into the aviator's death. Harm's past as a naval aviator is a source of friction to some of those on board the ship.

Aboard a decommissioned Naval vessel, inspectors discover the skeleton of a missing aviator. Harm and Mac investigate. Harm finds an important book, which contains a clue about the whereabouts of his father, but the book disappears.

Bud Sr. and Mike (Bud's father and younger brother) travel to Washington for Bud and Harriet's wedding. Bud Sr. leaves insults, injuries, and hurt feelings in his wake; Harriet's mother also causes much discomfort and embarrassment. Bud passes a big career milestone with grace and empathy. A dry cleaner loses Harm's dress whites, but Harm finds them in an unusual place. The girls go to Harriet's party, then Mac bails Harm, Bud, and the admiral out of a DC jail after Bud's party. Bud Sr. skips the beautiful wedding, and Mike arrives late. Harm takes charge of a detail of eight officers who form an arch of swords for the new couple; he also shows up with an unusual and unexpected date.

Three men sailors waylay a bar owner, and one of them beats him, supposedly in revenge for the rape of a fourth sailor, a woman, who accompanied them on a previous visit. Harm and Mac prosecute, and Mic and Bud defend. Harm figures it out.

After being promoted, Bud's first case as an attorney is defending his father "Big Bud" Roberts (Jeff MacKay) from charges of fraud and larceny, with Harm as the prosecutor.

Again at The Wall at Christmas, Harm meets Jenny Lake, a singer who, as a member of a USO troupe, entertained aboard Harm's father's carrier. She tells about their brief friendship. The JAG characters play other roles during flashbacks.

During an exercise, friendly fire goes too close to a boat hauling 15 Marines, apparently due to a mistake by PO Mike Roberts, Bud's brother. One by one Bud, Mac, Harm, the admiral, the SecNav, and Webb all fly out. Harm solves the puzzle.

A U.S. frigate collides with a Turkish destroyer in the Aegean partly due to a nearby Greek escort. Chegwidden ordered to prosecute the frigate's CO. Harm and Mac defend him. In DC, Bud's brother has a 19 hour date with Gunny's sister.

In Mazatlan, Mexico, Mike, Bud's brother, becomes involved in a barroom fight with a local, who later dies. Harm and Bud, with help from Bud Sr., eventually discover the cause. Mac successfully defends a Marine bulldog in a paternity suit.

Sarah dreams about an actual conspiracy to commit a mutiny in 1842 at sea aboard a brig of war, a sailing vessel, of the US Navy.

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.

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.

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".

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.

Harm, with a former client, flies for the CIA; they fix a problem in the Philippines, and they escape. Harriet has given birth to another son, and she and Bud hold a christening party. Midn. Mike Roberts helps a friend at the Naval Academy.

A sailor dies at sea; another sailor is blamed; Harm and Mac investigate; Mac prosecutes, and Harm defends. The admiral asks Coates to plan the wedding, but she overdoes. Harriet coordinates for a USO Christmas tour, and Mike meets a girl.

Harm's petition for a guardianship meets ups and downs; Mac tries hard to help. The admiral has trouble with a gift for Meredith, and Coates lends a hand. Sturgis stews, and he meets a new friend; his father preaches a Christmas sermon.

In Iraq two F-14 Tomcats bomb a hospital, which Iraqi forces have turned into a bunker; 32 civilians die. The SecNav stands trial in the International Criminal Court; Harm, Mac, and Bud defend him. Little A.J. disappears and reappears.

After dinner at a Chinese restaurant the gang takes part in a round of what might have become if the various people had set out on different roads. They wind up at a party at Harriet's castle, and they see one another in a different light.

A kilo of heroin disappears during the seizure of a foreign ship. Harm and Mac investigate; they find the missing kilo, then they find the culprit. Bud helps a Marine with a recording contract who now must deploy. Bud and Mike talk again.

The season finale finds cast members in a total state of change: Admiral Chegwidden reveals a surprising decision he has made; Mac is given some news about her health and Harm is faced with a personal loss.

A midshipman of the Naval Academy becomes lost overboard from a sailboat in a storm. The coach, a commander, goes to a pretrial hearing on a charge of dereliction of duty; Mac prosecutes, and Sturgis defends. Mattie moves back home.

Three MPs at Gitmo go on trial for injuring a detainee; the prisoner is a member of the US Army in disguise; Mac prosecutes, and Harm and an Army lawyer defend. Bud slugs a mouthy civilian and goes on trial; Sturgis defends him.

Coates runs into trouble with two former friends from her previous life, and Harm becomes involved. A rich civilian has bought an F-18, and his daughter, a Naval aviator, gets into trouble for having taught him to fly it; Bud investigates.

Pirates have seized a Burmese freighter in Indonesian waters; the US Navy becomes involved; Mac and Greg, the new lawyer, take part, and they avert a disaster. Bud and Harriet host a party, where Mike meets the general's daughter.

Harm and Mac get separate transfer orders; Harm gets a promotion. Vic investigates and resolves a fraudulent enlistment. Harm and Mac talk, then propose to each other; Bud flips a coin to decide which of them will resign from the service.