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.
A CIA mission sends Harm & Beth O'Neil 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 & Beth must land on the only available landing strip... the U.S.S. Seahawk.
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 inadvertantly 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.
Due to overloaded JAG caseload which was made worse by the review of all of Cmdr. Imes cases, the Admiral has the SecNav re-instate Harm's Naval Commission, clearing the way for Harm to return to JAG.
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.
A soldiers finds himself being investigated when his claim of killing an Iraqi prisoner makes the news.
The death of a sailor repairing the ships radar dish leads Mac to prosecute and Harm to defend the sailor charged with the death.
Harm attempts to gain legal guardianship 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 cuddled, its up to Mac to defend the suspect - a male petty officer who was intoxicated and has absolutely no recollection of the entire evening.
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. At the end, the court finds the USA on the following charges: Crimes against humanity - Not Guilty War Crimes - Not Guilty Intentionally targeting non-combatants - Not Guilty Willful destruction of civilian property - Guilty.
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.
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.
Mac continues to be tormented by her feelings over her having to hug Sadik Fahd, which begins to interfere with the other parts of her life - including her defense of a former Marine.
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 helps protects 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.
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.
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.