When a Marine colonel defies orders from superiors, as well as the State Department, and rescues his men who are being held and tortured by a Haitian warlord, he is court-martialed. Harm and Mac are assigned as prosecutors and are shocked when they find they must go head-to-head with Chegwidden.

Bud was put in a position to choose which side to go on. He choosed Admiral Chegwidden

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.

Admiral Chegwidden investigates the apparent suicide of his mentor, Admiral Clancy, who allegedly shot himself while on a hunting trip with several friends. Chegwidden can't believe that his friend would kill himself, and discovers that someone else may have actually pulled the trigger.

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.

(The time is 1980, several Russian soldiers are guarding a prisoner who is Harmon Rabb, Sr. at a train station. The KGB take a photo of the persons gathered there - a photo which has made its way to Harmon Rabb, Jr. in the present time.)

Clayton Webb meets with Harm at JAG and tells him who the men in the photo are. Webb mentions that one of them, Victor Lushov is now working in San Diego. Harm requests from the Admiral to take an F-14 hop to San Diego to visit his mother, keeping secret his true intentions.

In San Diego, Harm meets with Lushov who turns out to be a Russian pilot who was instrumental interoggating Harm, Sr. after he was shot down over Vietnam, later befriending him. He tells Harm Jr. all about what happened to his father, that Harm Sr. fed all kinds of disinformation to the Russians, which was worse than telling them nothing. Lushov gives Harm Jr. the KGB file number for his father. And says he wants to live and will not repeat what he has said to anyone.

Millions of viewers are turned into witnesses when they see a Marine guard shoot an arrested terrorist on live television, and its Harms job to defend him. With Mac on the prosecution, she and Harm are pitted against each other in what seems like an open and shut case of cold-blooded murder. But when Harm is replaced by a civilian attorney with a defense plan that doesnt add up and whose fees are being paid by a wealthy right wing industrialist, Percival Bertram. Harm decides to do some investigating of his own.

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.

When Navy SEAL Medal of Honor winner Lt. Curtis Rivers is fired upon while on a training mission, he returns fire only to discover that he has shot a seemingly unarmed 14-year-old boy. During Harm and Mac's investigation, they discover that the boy may have been accompanied by his uncle, a fugitive wanted by the F.B.I.

When Rivers goes AWOL to track down the fugitive and is captured by separatists, Harm and Mac find themselves not just investigating the case, but trying to defend Lt. Rivers in a court that does not recognize the U.S. government and its laws.

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.

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.

As lowest ranking lawyer at JAG, Bud is assigned to accompany Raglan, a former special Forces operative who is hired by the Pentagon to test security at military bases. Raglan's current mission is to test the security around a U.S. nuclear attack submarine. But when Raglan goes too far and hijacks the sub with Bud on board, Harm is called in to chase the sub down by second guessing his old friend. The cat and mouse game becomes deadly, though, when it appears that Raglan has switched sides, demanding millions of dollars in ransom or he'll take aim on a U.S. target.

Lt. Elizabeth ""Skates"" Hawkes, Harm's former RIO (radio intercept officer), comes under fire after the crash landing of a Tomcat aboard the USS Patrick Henry. The ship's captain and Skates' commanding officer both place the entire blame of the crash on her shoulders and press for her court-martial.

Barred from the initial investigation because of his relationship with Skates, Harm is finally able to help when he's called upon to defend his friend at her court-martial and employs all of his legal skills to save her military career.

Trouble in the JAG office starts when Gunnery Sgt. Victor Galindez, ""Gunny,"" is charged with assault following an off-duty altercation outside a gay bar. It comes to light that P.O. Tiner was also involved in the brawl, having come to the aid of his companion, whom Gunny was roughing up.

Meanwhile, Mac finds herself wrestling with the ""don't ask, don't tell"" policy as attitudes toward Tiner change around the office under suspicions that he's gay.

Mac prosecutes a SEAL jumpmaster is charged with causing the drowning death of a trainee during a parachute mishap by being hung over and is defended by Bud, assisted by a new female Lieutenant who is very ambitious, wanting to be the first female JAG.

Bud & Lt. Singer discovers a safety file that is inadmissible in court that supports the prosecution's contention that the jumpmaster was impaired. The file mysteriously winds up in Mac's car and she thumbs through it. After conferring with Harm who tells her what she already knows, she burns the file. But during questioning court, Lt. Singer objects that Mac is basing her argument based on the file, which Bud reluctantly agrees. Mac is charged with prosecutorial misconduct, removed & replaced by Harm.

Having been chewed out by the Admiral, she takes some leave & heads to spend time with Mic in Australia, running into the Admiral & Dr. Walden who are taking their own weekend 'trip'.

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

Harm & Mac square off in court over a charge of illegal fraternization, but when they oral arguments become directed at each other & reflecting their own relationship, Judge Helfman recesses the court for the day with a strong admonishment to the both of them.

All the staff shows up at Admiral Chegwidden's house for Mic & Mac's engagement party. Lt. Singer shows up in a knock-out of a dress which stuns the Admiral for a moment, not used to seeing her in civilian clothes.

Bud shows up dress properly for once, but Harriet notices after arriving that he has peanut butter on his tie. Bud is mortified trying to get a tie from anyone, without much luck. Later, he is forced to remove his jacket when wine gets spilled all over him. Even more mortified, Bud feels desperately out-dressed.

Throughout the evening, Mac reminisces with the Admiral about past events involving the both of them.

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.

Guards at Guantanamo Bay are ordered to remove a detainee from his cell for interrogation. He resists, so the guards try to subdue him and end up putting him in a coma. It turns out the "detainee" was a disguised soldier and the whole thing was a training excercise. Harm is assigned to defend the guards while Mac argues that torture and excessive force are not appropriate even when dealing with terror suspects. Back in Washington, Bud and Mikey Roberts go shopping for shoes and get into a disagreement with another customer that escalates into violence.