Sturgis is the acting JAG of the Navy. Simon tells Mac that Webb is alive. Mac visits Kershaw and Clay's mother, then Harm, Mac, and Simon go to Manderley, where Harm finds Webb. Clay's mother fixes a problem, and Mac breaks off with Webb.
In Iraq a firefight breaks out with friendly forces on each side; one Marine dies; each side says that the other side fired first. A retired Marine stands trial; Mac prosecutes, and Harm defends. Harm identifies the real trouble.
In a retrial after 22 years Sturgis prosecutes, and Harm defends a man, a young seaman at the time, who was wrongfully convicted of murder. Meanwhile Mac prosecutes, and Bud defends a chief warrant officer with four wives and families.
A Marine colonel undergoes unusual scrutiny while under consideration as the next JAG of the Navy. Harm and Mac investigate a shooting during a dispute between a US fishing boat and a Canadian one. Mattie and Jennifer talk about fathers.
MGen. Creswell has taken charge. An official of the DoD has died in Iraq; a Marine staff sergeant goes on trial for involuntary manslaughter by culpable negligence; Harm prosecutes, and Mac defends. Officers take partial responsibility.
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.
A biowarfare expert disappears, apparently by suicide; Harm, Mac, and the FBI investigate. A woman Marine has filed a petition to allow women to compete with men in boxing; Bud investigates, and the general changes his mind in a ring.
A wreck sends Mac to a hospital; while unconscious she dreams about recent events in her life, especially ones involving Webb and Harm. An EMT calls Harm, who goes to Mac's room; Harm and Mac start reaching and communicating.
An F-14 crashes while kids watch from the playground at their school; Harm investigates, and he gets answers. Bud's anger-management course degenerates into a fight. Mac beats the general during an annual requal on a pistol range.
At the Naval Air Station, Key West, Florida, a sailor goes on trial for murder; Mac prosecutes, Harm defends, and Coates serves as the sixth juror. The trial goes awry, but Harm figures out the murder. Bud helps by breaking a code.
A Marine captain has deserted and has become a freelance warlord in Afghanistan, seeking Osama bin Laden; the Afghan government places him on trial; Harm and Mac defend him; Islamic justice follows. The Navy recalls Bud Sr. to active duty.
In a firefight Taliban insurgents kill a Marine private first-class who has spent the three previous days with a Navy psychiatrist; the company commander of the victim accuses the shrink of medical malpractice by sending the Marine back into battle too soon; Harm and Mac investigate; the matter goes to a court-martial; Mac prosecutes, and Harm defends; the trial raises questions about official procedures. Bud defends a commander who has refused to surrender his position as the commanding officer of a frigate after BuPers ordered his relief for cause due to a collision...
A Navy helo damages an Iraqi fishing boat; Harm does his carrier quals in the F-18 Hornet, and he destroys a small Iraqi aircraft; and a Marine gunnery sergeant commandeers an Iraqi civilian SUV. Everything works out, and justice prevails.
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.
While delivering relief supplies, a Marine hits a local man; he goes on trial; Mac prosecutes, and Greg and Tali defend. The annual JAG conference meets in San Diego. Mattie is in serious condition after an aircraft collision on the ground.
Vic defends a Marine in Iraq, and he sees combat and takes part in it. Mac advises and encourages the general's daughter, who's a plebe at the Naval Academy. Harm continues his vigil with Mattie, who remains in a coma.
An explosion in Iraq kills 17 Marines in a reserve unit from a small town; one survives and returns home. The USMC Reserve Center burns due to arson; the survivor goes on trial for the fire. Mac goes to Iraq and investigates the explosion.
A Navy physician is in trouble for having given to an Iraqi child a drug in short supply. The general's brother, a SEAL in SE Asia, believes that a recently discovered body is that of a helo pilot who died while saving the brother's team.
A sailor dies during a fight aboard a ship at sea; Bud discovers the explanation. A seaman releases two dolphins from their pen; justice prevails. Mattie wakes up and talks. The general announces a reorganization, orders, and a promotion.
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.