Mac is unable to accept the news that Clayton Webb really is dead and ends up in possible danger looking into Webb’s "death". With the retirement of Rear Admiral A.J. Chegwidden, Cmdr. Sturgis Turner is named Acting Judge Advocate General.

When a Marine is killed in Iraq as the result of "friendly fire", Harm & Mac investigation results in possible involvement by a private military contractor.

A Naval Academy sailing team (that includes Bud's younger brother Mikey) is fighting a squall during practice when a female sailor is swept overboard and drowned. The JAG staff investigate whether the Commander was negligent when he ordered his team to sail through the squall.

Guards at Guantanamo Bay are ordered to remove a detainee from his cell for interrogation. He resists, so the guards try to subdue him and end up putting him in a coma. It turns out the "detainee" was a disguised soldier and the whole thing was a training excercise. Harm is assigned to defend the guards while Mac argues that torture and excessive force are not appropriate even when dealing with terror suspects. Back in Washington, Bud and Mikey Roberts go shopping for shoes and get into a disagreement with another customer that escalates into violence.

Coates gets an unexpected visit when a friend from her criminal past shows up looking for a place to stay. A Naval aviator is in trouble for giving flying lessons to her father, a civilian who just bought an F-18. Bud intervenes on her behalf

It's Christmas Eve. Col. MacKenzie crashes her car on the way home, and while unconscious through a series of episode flashbacks and discussions with a base therapist deals with many of her issues including infertility, insomnia, loneliness, Webb, and Harm..

Harm looks into the crash of a F-14 Tomcat

Harm and Mac are assigned to a case in south Florida involving the shooting death of a local car dealer's son outside a popular bar. The Gen. requests that P.O. Coates be allowed to go along and assist Mac. The jury pool of base personnel is quickly depleted as almost everyone on the base knew the accused, his former and very popular girlfriend, or had formed an opinion about the case. As a result Coates is forced to sit in as the Sixth Juror.

A Marine Captain is AWOL and working with the Mujahideen, he is accused of murdering several Afghan civilians. Harm and Mac are sent there to bring him in. Big Bud meanwhile is called up for service in Iraq but doesn't want to go and asks Bud for help..

A Navy psychiatrist in Afghanistan is accused of malpractice after a soldier under her care is killed in battle. Bud handles an age discrimination suit involving a Navy commander.

When Harm is forced to shoot down a civilian plane flying in a "no-fly" zone in the Persian Gulf, Harm once again finds himself on the wrong side of the court-room.

A US navy vessel makes contact with a ship that has been taken over by pirates. Mac and Vukovic are sent to negotiate the release of the hostages. Back in the States Commander Roberts and harriet open up their house to celebrate the birth of twins.

There is a huge snow storm in Falls Church so General Cresswell decides to have the Jag confrence in San Diego. Lt Makefield, Lt Vukovic and Mac go to San Diego Rabb stays behind as acting Jag in his place. Also as a result of the snow storm, Mattie is injured in an accident.

A marine Private kills a seemingly unarmed civilian in a raid on a Mosque in Karbala, Iraq. Lt. Vukovic goes to Iraq in order to defend the marine -- a hard task as the whole incident was filmed by a ZNN reporter. Meanwhile, Cresswell asks Mac to talk his daughter out of her plans to abandon a military career, and Harm maintains his vigil at Mattie’s bedside.

Mac goes to Iraq to investigate a bombing that killed a group of Marine reservists, while Harm and Bud go to Oklahoma to assist their families, but end up prosecuting the sole survivor, who is accused of starting a fire that destroyed the Marine Reserve Center.

Gen. Cresswell’s brother believes that remains found of a Vietnamese soldier are those of a helicopter pilot who saved his life during the war. Vukovic and Graves end up going to the South in search of a relative of the man’s for a DNA match. A Navy doctor is court-martialled for giving an Iraqi child medication against orders; the medication was in short supply and her Commanding Officer wanted to save it for wounded Americans.

Harm and Vukovic are teamed up to defend a sailor accused of manslaughter. Bud is assigned to prosecute what soon becomes dubbed "the dream team." At the end of episode it seems that Harm and Vukovic hold the ace but Bud has a surprise for them. General Cresswell then informs Mac that she is being posted to San Diego and Harm that he is being posted to London.

Gen. Cresswell informs Harm and Mac that they are being reassigned. Harm to London and Mac to San Diego. They both have the option to take someone from the office with them. They both ask Bud, but Harriet is worried about moving. With their deadline quickly approaching. Harm and Mac must sort out their lives and resolve their feelings for each other. Harm and Mac both reminisce about times past. And it all ends with a coin toss. Vukovic is trying to solve his own case.