Harm meets with a Russian 'contact' in order to purchase documents that will prove his father was taken to Russia after being shot down in Vietnam. However, during the transaction, they are interrupted by a KGB agent, Col. Parlovsky who shoots & kills the Russian, then runs off as FBI agents show up, finding Harm over the body, with the gun & documents he wrestled away.

As the FBI wants to hold him for the murder of the Russian, Adm. Chegwiggen manages to have Harm transferred to a military brig, and court-martialed, much to the dismay of the FBI agents. CIA agent Clayton Webb, knowing that it was Parlovsky, not Harm that committed the shooting, arranges for Harm to escape from custody in hopes Parlovsky will contact Harm.

In the end, Parlovsky makes contact with Harm, but they both get away before Webb can catch them. Parlovsky tells Harm the documents were a fake and burns them. He then leaves, refusing to help clear Harm of the shooting.

Harm's skills as a lawyer are challenged when he defends a female ensign who claims she murdered an officer because her ""instincts"" told her he meant to hurt her.

The ensign claims that when the officer entered her apartment on false pretenses, she felt threatened by him and killed in self-defense. Though the defense is decidedly thin -- no weapon was even found on the man's body -- Mac and Harm decide to stick with the case and are determined to help the ensign remember forgotten details of the event.

Following her ugly break-up with Dalton Lowne, Mac has reason to believe that he's stalking her -- until he's killed during an apparent car-jacking and the stalking continues. Much to Harm's dismay, the strain of the two events pushes Mac to the edge -- and to the bottle. Concerned for Mac's safety and sobriety, Harm intensifies his search for Mac's tormentor before he causes her bodily harm.

Bud has his hands full when his obnoxious and abusive father, Big Bud, and his younger brother, Mikey, arrive in town for his wedding. Big Bud throws a stag party at a boisterous strip club where Harm's dress whites end up on the body of a stripper. A fight breaks out and Harm, Bud and Chegwidden find themselves in the slammer on the day of the wedding.

While Mac goes downtown to bail them out, Harriet begins to have second thoughts about the imminent nuptials.

Mac is arrested and placed on trial for a major felony, along with her former commanding officer and mentor, Col. John Farrow. Conviction could result in long prison terms.

Harm volunteers to defend her, but his efforts are thwarted by Farrow's defense attorney, JAG exchange officer, Australian Navy Commander Mic Brumby. Harm feels that neither defendant has come clean with the truth and he begins to search for evidence which is not forthcoming from either one. Ultimately, he learns that Mac and Farrow have each been trying to protect the other. The key witness in the case turns out to be a major surprise to both defendants.

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.

With Harm's eyesight fixed, Harm decides to go ahead and submit a request to be transferred to a fighter squadron. When Lt.Cmdr Parker finds his written request, she is upset at the prospect of Harm being gone for months at a time.

Afterwards, Harm goes over to Mac's apartment who has Chloe spending the night with Mac before she is reunited with her real father. Harm informs Mac of the eye surgery and his plans. Mac is equally upset at the prospect of losing Harm. Mic shows up at Mac's apartment after Harm leaves attempting to court Mac's feelings. After Mic leaves, Chloe tells Mac that Brumby and Harm have a crush on her and begins teasing Mac: ""Harm & Mac, sitting in a tree, k-i-s-s-i-n-g.""

Admiral Chegwidden passes Harm's request to be transferred onto the SecNav. Not willing to do any favors for Harm, the SecNav is reluctant to intervene.

Admiral Chegwidden welcomes Harm back to JAG by assigning him a tricky case - defending the son of the Secretary of Navy. Harm takes the case when Lt. Nelson, the son of the Secretary of the Navy, is accused by Cmdr. Burke of disobeying an order at sea, an act worthy of a court martial.

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.