The 9th season begins where last season left off, with Harm, Mac, Webb & Gunny still in Paraguay searching for the terrorist Sadik. Their search is complicated by Harm’s feelings being tangled up which drove him to resign his commission & rush to South America in the first place.

Harm returns to Washington, DC and is shocked to discover that Admiral Chegwidden had actually processed his resignation through official channels. Also, a female petty officer listed as missing in action during Desert Storm is located in Iraq, married to a bedouin sheik. As a result, the Navy charges her with desertion.

Harm finds his first mission flying for the CIA takes him to the Phillipines where he must "drop" a limo. Back at JAG, "Mikey" Roberts calls on Mac to help him when he must act as a character witness in a honor code conflict.

While conducting a flight test, Harm ends up involved in a serious CIA mission, over North Korea. In Iraq, a Marine recon platoon is surprised by a 10 year-old Iraqi unarmed civilian tending to his goats. Surprised at seeing the armed Marine, the boy runs off. Later the platoon is involved in a skirmish, resulting in two deaths and the Sergeant losing their radio. Unable to call in for transportation out of the desert, the platoon must end up walking many miles in the desert to safety. Once safe, it is learned that the firefight was the result of the boy returning to his village & notifying some of the local Iraqi resistance members, who immediately went out to engage the platoon.

A CIA mission sends Harm and Beth O’Neill to Libya to pull an agent out of that country. But when the agent wants Harm to transport the entire family, Harm has to modify his mission while avoiding contact with the Libyan authorities. When that fails and their plane comes under attack, Harm and Beth must land on the only available landing strip ... the USS Seahawk. At JAG, a Marine is accused of being involved with the Al Qaeda terrorist organization and Mac is assigned to defend him.

Harm is shocked to find that his life is making another unplanned turn, when he is notified that he is fired from the CIA for being inadvertently shown on the cable news network ZNN carrying a young girl after landing on the USS Seahawk. Unemployed once again, Harm takes up crop-dusting to pay the bills. At JAG, Commander Carolyn Imes, who once worked at HQ-JAG (when she was a Lt. Cmdr), is brought back to HQ from overseas duty to fill the vacancy created by the departure of Cmdr. Rabb. But it’s Bud and Mac who are shocked when they learn that their old colleague falsified documents and has been practicing law without passing the Bar Exam. And Catherine Gale "shocks" Harm with the news that she is pregnant.

Due to the overloaded JAG caseload, which was made worse by the review of all of Cmdr. Imes’ cases, the Admiral has the SecNav reinstate Harm’s Naval Commission, clearing the way for Harm to return to JAG. When a US submarine rescues 10 North Koreans after their vessel sinks in South Korean waters, Cmdr. Turner arrives from Washington to determine their purpose.

A Marine helicopter pilot finds himself under investigation when he intervenes in a civilian law enforcement hostage situation and puts an end to the hostage crisis. Harriet is put in charge of organizing a Christmas USO show in Iraq.

The death of a sailor while repairing the ship’s radar dish leads Mac to prosecute and Harm to defend the sailor charged with the death. At the Naval Academy, Mikey Roberts’ friendship is tested when his roommate introduces him to his sister and the two of them hit it off, causing fireworks between Mikey, his roommate and his sister Cassie.

Harm attempts to gain legal guardianship of Mattie, but finds his past single "lifestyle" may pose a problem in making good on his promise to her.

As Harm now has custody of Mattie, PO2 Jennifer Coates agrees to move into an apartment down the hall from Harm. Admiral Chegwidden looks into why the diamond he gave to Meredith for their engagement "just doesn’t look right".

When a female Naval officer is found brutally murdered, its up to Mac to defend the suspect - a male petty officer who was intoxicated and has absolutely no recollection of the entire evening. Also, a Navy SEAL Commander finds himself facing charges of larceny and fraud - his victim: the United States.

When civilians are killed in a bombing raid, an International Criminal Court charges the United States with war crimes and the SecNav is the one on trial representing the USA. The SecNav is defended by Harm, Mac & Bud who find they must also defend the United States decision for waging the war. Back in the USA, when Bud has to fly overseas to help defend the SecNav, Mike is asked to babysit little AJ. When little AJ disappears, Bud flies back to the USA in the middle of the trial.

The crash of an aircraft into an aircraft carrier is believed to be the result of the pilot committing suicide, which has Harm & Mac squaring off against one another; especially as Mac wants to hold the pilots commanding officer responsible when she learns he knew the pilot was deeply depressed before the pilot took off. When Mattie gets in over her head, she needs Harm & Petty Officer Coates to help her get out of it.

Sadik Fahd who held Mac & Webb captive in Paraguay at the end of last season, shows up in Washington, DC and Mac has to wonder what he’s up to when he begins to contact her. Harm temporarily loses his hearing when the car battery on his Corvette explodes while he was working on it.

Mac continues to be tormented by her feelings over her having to kill Sadik Fahd, which begins to interfere with the other parts of her life - including her defense of a former Marine. Mattie continues to deal with how she feels toward her father.

Members of the "JAG" staff are "helped" along to discover their true inner feelings while celebrating Jennifer Coates promotion to Petty Officer 1st Class.

Mac learns to be careful what she asks for - as she is assigned to escort a female Marine prisoner, after having made the request that the prisoner should be escorted by someone able to control her

Cmdr. Turner defends himself against the complaint filed against him for displaying anti-Korean attitudes when assigned to deal with the SARS outbreak earlier. Harm & Mac go up against one another in the case of a Marine General making public speeches stating Islam goes hand-in-hand with evil & terrorism.

Harm helps protect a mother of a marine killed in action while serving in Iraq from overzealous reporters. In so doing, he works to prepare her for the upcoming burial of her son. Mac & Bud are called upon to see why armored vests given to soldiers in the field to protect them, instead are failing to do what they were designed to do.

Navy SEAL’s come under the microscope when a large amount of heroin is intercepted and confiscated, only to have a kilo of it turn up missing. And Bud comes to the aid of a Marine singer who is being harassed by the record company that he is under contract to, when they object to him serving in the war.

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.