Bud's first case as a newly sworn in JAG attorney is to defend his father, a retired Navy Chief who's been accused of having been involved in defrauding the Navy when he was in charge of Ship's Stores. Though the two have been estranged, Bud feels a strong obligation to his father, who specifically requested him to be his attorney. Harm is the designated prosecutor, which spooks Bud, as he knows he's going up against the best.

Bud's underachieving brother is accused of making a mistake during a training exercise that nearly killed 15 Marines. But establishing his innocence proves to be a difficult task, thanks to the age-old tension between the Navy and the Marines.

Adm. Chegwidden frets over a speech he must give when he is to be given an award.

Mic Brumby returns unexpectantly to the States; Mac & everyone are stunned when he announces that he has resigned his Royal Australian Navy commission so that he could move to the USA and be by the "woman he loves."

When U.S. and Turkish ships collide during a NATO exercise, Harm and Mac defend the U.S. captain, who is being made the scapegoat for political reasons.

As Bud is defending his brother Mikey, a petty officer accused of murdering a Mexican in a barrom brawl, their father shows up.

Preparing to give a lecture about an 1842 Naval court-martial, Mac finds herself daydreaming about what actually happened.

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.

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.

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 court orders the USA to provide reparations to the town of Tikifa in the amount of $20 million US dollars. The prosecutor mentions to the SecNav that he doesn't agree with the verdicts, but pleased the SecNav won't have to go to prison. In response, the SecNav states that the two countries have been friends for too long and they both go off to get a drink together.

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

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.

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.

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.

General Cresswell informs Harm and Mac that they are being reassigned. Harm to London and Mac to San Diego. With their deadline quickly approaching. Harm and Mac must sort out their lives and resolve their feelings for each other.