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 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.

A Marine dies in an ambush in Iraq; his sister is a classmate of Mattie; Harm and Mattie help the mother and the sister of the Marine. Bud investigates the failure of the body armor. Harm and Mattie continue to understand each other better.

During a guest sermon a Marine general has made remarks about the Islamic faith; this publicly boils into a court-martial; Mac prosecutes, and Harm defends. Bud investigates a complaint of racial bias against Sturgis, and he resolves it.

Mac discovers the reason for a false positive result of a drug test for an angry woman enlisted Marine, and Harm and Bud represent a senior chief petty officer who is HIV-positive, and whose privacy has become compromised.

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 discharged Marine is recalled to active duty to stand trial for the unauthorized wearing of a Silver Star; Harm prosecutes, and Mac defends. The admiral sends Mac to see a shrink. Bud loses a snake. Harm and Mattie have ups and downs.

A battery explosion deafens Harm. The CIA's diamond expert, Van Duyn, disappears, along with 24 of the Navy's synthetic diamonds. Sadik returns and plans new terrorist attacks, but Mac intercepts him and takes care of him and his plans.

A crash aboard an aircraft carrier appears to be a case of the pilot committing suicide, and Harm and Mac face off when Mac wants to hold the pilot's CO responsible.

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.

Mac must defend a petty officer accused of murdering a female officer, but the man has no memory of the night in question, while a Navy SEAL who purchased nerve gas needs Bud's help to avoid prison.

Adm. Chegwidden launches an investigation into the illegal diamond trade when he discovers his fiancee's stone might have been smuggled.

Turner faces charges of racial bias; Harm petitions the court to get custody of Mattie Grace; Coates tries to engineer a Christmas miracle for Adm. Chegwidden & Lt. Sims.

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.

A Marine claims to have killed an Iraqi PoW; Bud prosecutes, and Mac defends. During a baseball game a pitcher hits a batter; the pitcher faces a charge of assault; Harm prosecutes, and the admiral defends. Harm stays in touch with Mattie.

A Marine helo gunship intervenes during a standoff at a ranch; Mac prosecutes the pilot, and Harm defends. Bud investigates a Naval Reserve physician who, a conscientious objector, has received his medical education at Navy expense.

Sturgis helps a US submarine with 10 survivors of the sinking of a North Korean midget submarine, and Harm helps (as do Mac and the admiral) an underprivileged WW2-era Navy veteran with a legal problem. Harm stays in touch with Mattie.

Cdr. Imes never passed a bar exam; she goes on trial for fraud and conduct unbecoming; Sturgis prosecutes, and Mac and Bud defend. Harm flies as a crop-duster. Coates tries to get the admiral to take Harm back. Harm and the admiral meet.

With foreign civilian passengers Harm and Beth land a damaged C-130 aboard USS Seahawk. A Navy seaman, having converted to the Islamic faith, stands accused of taking part in al-Qaeda activities; Sturgis and Bud prosecute, and Mac defends.

A Marine faces a charge of dereliction after becoming lost in Iraq in a sandstorm; Sturgis prosecutes, and Mac defends. Harm flies again for the CIA, aboard a spy plane for a training hop, which turns into a real mission over North Korea.

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.

Webb, Mac, and Harm return from Paraguay. A sailor became MiA in the Gulf War 12 years before, and she reappears as a member of a nomadic tribe. Bud investigates in Iraq, then he prosecutes, and Mac defends. Harm interviews with the CIA.

Gunny takes Webb to a hospital, Harm and Mac survive a "hard landing", and they all rejoin in the city. Harm and Mac chase the Islamic drugs-and-arms dealer but fail to catch him; the two continue to examine and discuss their relationship.