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. Meanwhile, Mac is on the verge of making a deal with the traitorous Naval officer when he and his lawyer are murdered. Mac and Webb then discover that the traitor was linked to a Russian assassination plot. But Mac’s attempts to alert Harm fail, and he is caught in an ambush with a Russian who reveals the life-changing secret to him.

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. As Mac prepares for her televised prosecution of an innocent looking young ensign accused of murdering her husband’s teenage girlfriend, she learns that her opponent is none other than Juanita Ressler, who was her professor in law school. Ressler is a very media-savvy trial attorney who uses every trick in the book to swing the media and the public over to her client’s side. Harm travels out to sea to investigate the death of a sailor aboard a carrier. Originally thought to be a suicide, Harm discovers evidence to the contrary.

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. When AJ talks to Dr. Walden about what happened to his car, she is appalled that AJ would accuse her son of impropriety & terminates their relationship. Danny Walden is quite smug to AJ that he had been able to break them up -- which will come to haunt him later. With his car still being held by the police, he is dismayed with driving a rental car. Harriet goes into labor 4 weeks early and a seemingly positive childbirth turns sour when it is discovered that the baby’s head is pressing against the umbilical cord cutting off blood supply to the baby and her doctor (Dr. Gettis) is nowhere to be found. As another doctor steps in, Harriet is wheeled to the operating room in an attempt to save the baby. However, even after the arrival of Dr. Gettis, the medical staff was unable to save baby Sarah.

Harm and Mac defend Adm. Tom Boone in court against the charges that he was responsible for massacring civilians during the Vietnam War. Although he is eventually acquitted, he decides that it is probably best to retire from the service, despite Harm’s objection that the Navy needs men like him.

Mac becomes "Acting JAG" as Admiral Chegwidden is selected to head the Promotions Board for Captain. Harm takes up the defense of a former Marine Drill Instructor who is facing life imprisonment under the 3 strikes law. Cmdr. Ted Lindsey (last seen in "People vs. Mac") tries to impress the Admiral & Mac in an attempt to earn promotion to Captain.

Harm defends a Sergeant Major accused of the attempted murder 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. Meanwhile, when Tiner hooks up a new screensaver that searches for extra-terrestial life on the Admiral’s computer, it stirs excitement when it starts making weird noises.

When an inept seaman’s apparent suicide aboard an aircraft carrier turns into a murder investigation, Harm and Bud try to find out what really happened. Mac deals with a bigamist client.

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 (and the world) that the accident was caused by a faulty new Russian torpedo, without divulging top-secret material. Meanwhile, Mac is sent onboard the USS Watertown to observe when the Congressional committee headed by Rep. Bobbi Latham investigates why women are not allowed to serve aboard submarines. Renee and Mic are left behind wondering whether there really is something between Harm and Mac.

Harm and Mac travel to Bahrain to determine if a female Marine found aboard a terrorist boat that attacked a U.S. Naval destroyer was coerced into helping her captors or was a willing participant. Sgt. Joan Steele, kidnapped by terrorists a month before the attack, insists that the cooperation she gave the terrorists was designed to foil their plot. Harm, who is defending her, finds her claim dubious. CIA Operative Clayton Webb asks for her help in tracking down a known terrorist who is planning to bomb another U.S. target within 48 hours, and Steele readily agrees. But then she suddenly disappears, confirming Harm’s suspicions and, more importantly, leaving the target -- a busload of American children -- at risk.

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

A Marine sergeant in prison needs Harm’s help again when his prints are found on a murder weapon. Bud is nervous when he is assigned to carry a briefcase with the nuclear launch codes.

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. Despite this evidence, Harm is unwilling to accept the premise that Jordan committed suicide & calls in Lt. Cmdr. Teresa Coulter to help examine the forensic evidence. Harm & Mac begin to look for possible suspects who would want to kill her, starting with her last boyfriend who had also been a patient of hers. However, as each of the suspects are ruled out, they begin to look for other possibilities to explain her death. The investigation leads to a shocking discovery for Jordan’s neighbor. Returning home, Harm is stunned to find a letter from Jordan in his mail. Jordan wrote & mailed it a few hours before she was killed; in which she tells Harm just how much she had valued their time together.

Admiral Chegwidden throws Mac and Mic an engagement party. Mac and Harm end up discussing the ups and downs of their relationship in private, with frequent flashbacks to previous episodes.

As Mac prepares for her wedding, she is upset when Harm tells her that he will miss the rehearsal dinner because he will be on the Patrick Henry doing his carrier landing qualifications, and Mac thinks he may miss the wedding as well. Harm is not worried, but an unexpected storm on the flight back puts his Tomcat in peril.