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.

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 its Bud & 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 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.

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 soldiers finds himself being investigated when his claim of killing an Iraqi prisoner makes the news.

During the all-star game of the Navy & Marine baseball players, a batter narrowly escapes being killed after being hit by a ball thrown at him by the pitcher. The pitcher then comes under scrutiny for possible assault charges.

The death of a sailor repairing the ships radar dish leads Mac to prosecute and Harm to defend the sailor charged with the death.

At the Naval Academy, Mikey's 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 & his sister Cassie.

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"".

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.

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.

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.

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.

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.

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.

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.

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.