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.

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.

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.

When Harm takes young Josh on a weekend cruise for Navy families aboard the frigate, pleasure turns to fear when the ship is taken over by terrorists who intend to fire missiles at Cuba. After Josh and Harm manage to elude the terrorists, they try to contact authorities about the situation. But the plan goes awry when Harm is found out, and he then tries to strike a deal with the terrorists while also racing to foil the plot before the innocent civilians get hurt.

(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.

Having been shot at by Russian fighters, Mac & Harm are forced to eject from their plane, which then noses into the bottom of a very deep lake. The Russians announce to the world that Harm & Mac have been killed, which is broadcasted back to the USA by ZNN reporter Chuck DePalma.

Webb tries to convince the Admiral that they have been killed, but when A.J. learns their bodies haven't been found, A.J. becomes irate and vows to go to Moscow himself to look for them. The SecNav orders A.J. not to go, who replies that the SecNav doesn't want to try & stop him.

In Russia, A.J. meets with DePalma who tells A.J. that he doesn't believe the Russians, that certain things in their story don't add up.

In the woods, a husband & wife gypsies come across Harm & Mac. They are disappointed when they learn that Harm & Mac are not American Spies as at least the spies have gold coins to give to Russians that help them.

Harm and Mac use a party at the Sudanese Embassy as a cover for their investigation of a kidnapping, and they're literally caught by surprise when terrorists take the visiting dignitaries -- and Mac -- hostage.

Meanwhile, Bud notices that Harriet seems to be suffering from more than just flu symptoms.

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.

When three U.N. peacekeepers are taken hostage in Kosovo, a SEAL team is sent in to rescue them before the end of a 24-hour deadline set by the terrorists. But when heavy ground fog delays the SEAL team by 30 minutes, the hostages are found dead and the team is blamed for their deaths. Mac and Bud begin to defend the team only to have Bud removed because of the defendants' lack of confidence in his legal expertise. Meanwhile, Admiral Chegwidden spends his vacation acting as technical advisor on a movie about the Navy and runs afoul of the Hollywood types who hired him.

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.