Mac is unable to accept the news that Clayton Webb really is dead and ends up in possible danger looking into Webb's "death".
When a Marine is killed in Iraq as the result of "friendly fire", Harm & Mac investigation results in possible involvment by a private military contractor.
Harm is asked to re-open a 20yr old case of a seaman accused of murdering a prostitute. He doesn't deny stabbing her but he didn't hug her. Harm finds out that a similar crime was committed and uses this to free the seaman who has been wrongfully imprisoned.
A Marine Colonel is on the President's short list to become the new Judge Advocate General sparking controversy while Harm & Mac investigate a Navy Ensign accused of shooting a Canadian fisherman.
When a US Senator is killed in Baghdad, fingers point to the squad that was sent to protect him prompting Mac and Harm to find out what actually happened.
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.
The car belonging to a Navy Commander assigned to a Bio-Weapons Defense Laboratory is found abandoned on a bridge across the Potomac River. Harm & Mac work with FBI agents in the investigation.
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 dealers 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 most 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 is charged with theft (stealing a car from an Iraqi), MG. Cresswell meets up with his old friend from Iraq but soon finds out that his friend is the father of the son that the Marine stole the car off of. 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 and a age discrimination suit are the cases assigned to Harm, Mac & Bud.
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.
Mac and Lt. Vukovic go to Indonesia to negotiate with a modern-day pirate for the release of Naval hostages. Meanwhile, Bud and Harriet have an open house in celebration of their new twin babies.
Part of the JAG team goes to San Diego. Harm stays back as acting JAG. While he is there, a huge snowstorm strikes and Mattie is injured in an accident. Meanwhile, Mac and Vukovic find themselves working close to each other on a case at Camp Pendleton.
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 South Vietnam in search of a relative of the man's for a a DNA match.
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.
Cresswell informs Harm that he is being relocated to London, Mac is being sent to San Diego, and they each get to bring one person from the office with them. With their respective moving dates rapidly approaching, Harm and Mac must figure out their personal lives, as well as their feelings for one another.