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.
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.
Mac is assigned the case by the Admiral despite Bud's plea to be the lead attorney. Even though he is ordered to stay away from the case, he nonetheless can't. Mac questions Dr. Gettis as to why he took so long to respond when Harriet labor was in trouble. Dr. Gettis claims that his pager battery had died & didn't realize he was needed until he heard the overhead page for him.
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.
Lt. Singer appears at the door during Kate's conversation and soon afterward, the affair is reported by the Washington media, although Harm suspects Lt. Singer as the source, she denies she overheard anything.
Eventually, Kate decides that Washington is just not the place to work and decides to turn down the Admiral's job offer.
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.
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 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.
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.
Meanwhile, Mac is sent onboard the USS Watertown to observe when the Congressional committee headed by Rep. Latham investigates as to why women are not allowed to serve aboard submarines.
Renee & Mic are left behind wondering whether their really is something between Harm & 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.
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.
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.
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.
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. At the church, Chloe is still wary of being friends of Mic. On board the USS Patrick Henry, Harm learns that the LSO who will be grading him thinks of him only as a "land-based Washington weenie." His fears that he won't be graded fairly are realized when he is ordered to land after his first attempt is waved off. After convincing the LSO that they were flying they way that the LSO taught them, he allows Harm to try again. After passing, he then completes his required night traps and requests to head back to Andrews AFB. With an approaching storm, all air operations are suspended, but is assured that he & Skates can be on the first Tomcat, once its forecasted to be safe. With a break in the storm, he & Skates are allowed to go.