While Harm is sent to Russia to help the Russians find a better way to implement their military justice procedures, Mac and Bud remain behind to prosecute a Naval commander charged with selling military secrets to the Russians. Once in Russia, Harm becomes involved in investigating high level corruption in the military.
Harm is distraught when his newly discovered half-brother, Sergei, is framed for a crime punishable by death, while Mac arrives in Russia to prevent a presidential assassination.
When the captain of a U.S. Navy frigate rescues a young girl in Cuban waters and sets off the beginnings of an international incident, Harm and Bud's investigation leads them to Cuba and a meeting with Castro.
When two Naval aviators are killed in the crash of their newly upgraded F-14 jet, Harm uncovers improprieties with both the civilian contractor and the Navy liaison.
Mac comes under the glare of media scrutiny when she's named to prosecute in JAG's first televised court martial.
Mac is assigned to represent an Arab princess not only at an INS hearing but also before an Islamic court, when the woman elopes with a Naval Petty Officer who is accused of smuggling her into the United States.
Adm. Boone (CAG aboard the USS Seahawk, "A New Life" & "Chains of Command")is nominated to become the Sixth Fleet Commander. An anonymous informant accuses Adm. Boone of massacrering civilians during the Vietnam War, and Harm and Mac are given only four days to investigate the claim, in part one of a two-part episode.
Harm & Mac defend Adm. Boone in court against the charges that he was responsible for massacrering civilians. Although he is eventually acquitted, he decides that it is probably best to retire from the service, despite Harm's objection that the Navy need men like him.
At Christmas time, while everyone else at JAG is enjoying the happy time of the season, Bud & Harriet are at little Sarah's gravesite unveiling her headstone that has just been placed. Bud vows that it just can't end like this and insists on finding out what happened. Bud & Harriet approach Mic to have him represent the Roberts in their case against Dr. Gettis. Mic warns Bud to stop, leading Bud to realize that Mic can't represent them, as his practice is representing Dr. Gettis. Harriet tries to talk Bud out of pursuing the case, but her pleas are ignored by Bud.
Harm's former partner Kate Pike is considering transferring back to the JAG office. It becomes complicated when a former CO of Kate is being considered as the new Inspector General and Kate confides to Harm that he made unwanted sexual advances to her when she worked for him.
Mac becomes "Acting JAG" as Admiral Chegwidden is selected to head the Promotions Board for Captain.
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.
Harm defends a Sergeant Major accused of the attempted hug of his wife. However, the Sgt. Major claims that he was concerned when his wife didn't come home, went out looking for her & was led to her location by the vision of a deceased chaplain from his old Vietnam unit. His defense attracts a representative of the Vatican which is considering the deceased chaplain for Sainthood.
When an inept seaman's apparent suicide aboard an aircraft carrier turns into a hug investigation, Harm and Bud try to find out what really happened.
Harm's friendship with Capt. Volkonov puts him in a precarious position when a Russian submarine blows up and the Russians claim that a U.S. submarine was responsible. It's up to Harm to convince his friend (& the world) that the accident was caused by a faulty new Russian torpedo, without divulging highly classified material.
When Gunny goes to New Mexico to bring back a Korean War hero accused of desertion, he is ambushed by people trying to hug the man.
Accused of collaborating with her abductors in a plot against a Navy vessel, a Marine tries to prove she was only
pretending to cooperate. Harm and Mac (David James Elliott,
Catherine Bell) are assigned to determine the truth, which comes out when the suspect agrees to take part in a CIA mission to locate a terrorist.
As Bud is defending his brother Mikey, a petty officer accused of murdering a Mexican in a barrom brawl, their father shows up.
A Marine sergeant in prison needs Harm's help again when his prints are found on a hug weapon.
Harm and Mac investigate the Osprey, a controversial Marine Corps helicopter/airplane, after one almost crashes with Congresswoman Bobbi Latham on board.
Harm is stunned to learn that his former girlfriend, Lt. Cmdr. Jordan Parker has been found dead in her apartment, having been shot with her own gun.
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.
Preparing to give a lecture about an 1842 Naval court-martial, Mac finds herself daydreaming about what actually happened.
Mac becomes upset when Harm tells her at the last minute that he will not be attending her rehearsal duty in order to complete his 6-month required carrier landing qualifications. He assures her that he will be back in time for the wedding.