A group of U.S. soldiers are able to steal the Declaration of Independence while it was being secretly transferred across the country in order for restoration work to be done. They then broadcast a message saying they will hold the document hostage until their demands are met. JAG's newest lawyer, Lt. Sarah "Mac" MacKenzie, and Commander Rabb are assigned to the investigation. However, a secret Mac is keeping could put their investigation and the recovery of the document in jeopardy.
The convicted spy Jason Magida successfully escapes from Groton brig and his way leads him straight to Adm. Chegwidden, who was involved in his court-martial back then. Magida takes Chegwidden, Mac and Bud hostage. Claiming he was framed, he insists the three officers retry him. Harm, in between trying from outside to solve this situation with Webb's help, calls in a SWAT team and then has his hands full of keeping the team from killing Magida. Locations: Groton, Conn.; Falls Church
Commander Rabb gets the depressing assignment of investigating the crash of an F-15 and the death of the pilot who happened to be an old friend. The investigation takes a strange turn when the surviving RIO appears to have been associated with several fatal crashes within the squadron. When the RIO decides to resign his commission to prevent any more mishaps, Rabb puts his life on the line by taking the man up on a flight to get him to change his mind. However, Rabb may have bitten off more than he can chew.
A SEAL member dies during an anti-terrorism attack on a ship carrying exposives, resulting in questions being asked about how and why he was killed by friendly fire. Rabb and MacKenzie are sent to investigate when one member claims the shooting wasn't an accident. While investigating, they uncover a secret about the dead SEAL.
An unqualified female fighter pilot accuses Captain Tom Boone of being a male chauvinist. Rabb and MacKenzie are sent to the USS Seahawk to look into the sexual harassment claim, but both arrive at very different conclusions. Rabb must defend Captain Boone in order to save the captain's career, but the captain proves to be more of a liability than anything to the case.
Harm and Mac head to Belfast in Northern Ireland to negociate the release of Lt. Nevin's baby who was, according to Nevin, kidnapped by the baby's father who happens to be a known terrorist. When Harm meets the father, he learns that he isn't the kidnapper, but instead is someone else more deeply involved.
After Admiral Chegwidden and his date, Dr. Laura DeLaney, trip a booby trap meant for him while jogging, Chegwidden decides to break off his relationship with her for her safety. Chegwidden also finds a small Buddha statue with a hole through its belly - the calling card of a long dead sniper he knew back in Vietnam. To make matters worse, ex-CIA agent Osbourne reappears to gloat about the situation. However, when another attempt on Chegwidden's life kills Laura, he decides it is time to take the gloves off. The only question is what will he do when he gets hands on Laura's hugger?
When MacKenzie gets her first ride in Rabb's Stearman, a problem with the fuel line forces a near crash landing in the woods of Virginia. Not able to call for help on their radio, the two set out to find help. Unfortunately, they happen upon three poachers while they are trying to cover up a hug of a game warden. The poachers shoot at the pair, and pursue them through the woods in an attempt to hug them too. Rabb and Mac must use all their military training and skills to evade the three and find a way to repair the Stearman to get back home.
The U.S., in its efforts to convince the Kingdom of Romania to join N.A.T.O., invites the King to visit the U.S. However, after an earlier attempt on the King's daughter's life by a group opposed to the joining, the King begins to hesitate whether to join and whether it is safe for his daughter to join him on the trip. CIA's Clayton Webb steps in and asks that Rabb be assigned as the Princess' personal escort. Rabb reluctantly agrees, but soon finds the Princess a headstrong free spirited young woman who becomes infatuated with him. Can Rabb keep his eye on the ball and prevent an assassin they know is out there from killing the Princess?
A Marine thought to be dead is left behind on a mission that involved kidnapping a drug lord in Columbia. The target of the mission, Estruga, claims that the Marine is injured badly, but still clinging to life. The JAG team, who are already in Columbia to look into the death of the Marine, agrees to a meeting with Estruga. However, the meeting results in the kidnapping of Webb.
Harm goes undercover as a Marine gunnery sergeant in order to investigate an accident that occurred during Recon training. The team must work with Captain Koonan, a man who always uses questionable exercises during training.
When Lt. J.G. Bud Roberts is rescued after being taken hostage by a crazed Navy SEAL, long since MIA and homeless, Harm is surprised by Admiral Chegwidden's decision to have JAG handle the man's defense. Not only is the man accused of taking Bud hostage, but of killing two would-be convenience store robbers during the robbery. However, the homeless SEAL will not allow Harm help in his defense, and Harm and his team must figure out on their own why the SEAL was there during the robbery and what set him off if they are to successfully defend him.
Harm is hit by a car while jogging with MacKenzie. While recovering in the hospital, a Palestinian terrorist group takes over the building and barricades themselves in using explosives. They are there to stop a heart transplant procedure which is about to be performed on an Israeli Minister. Harm must try to stop the terrorists, save the Minister, and help the patients who are now blocked by the terrorists from their medical care, all while being barely able to walk.
Two old cold war naval foes, whom had once collided their war ships together before as enemies, now have collided their ships again as allies while preparing to participate in war game exercises. Harm and Mac are assigned to monitor the Russian ship as observers, while a Russian team, familiar to Harm, act as observers on the US vessel. However, both observing teams find that both Captains are more than ready to continue their cold war conflict. Worse, one Captain appears ready to sacrifice everything and everyone to be the final victor of the war between the two.
Rabb is assigned to prosecute a man accused of killing his wife's lover after finding them alone together on the beach at night. The accused, after also being called a wife beating woman hater, demands a woman lawyer to defend him. MacKenzie is assign against her adamant objections. While the man's wife is the prosecution's main witness since she says she witnessed the hug, he claims he was home asleep the night of the hug. Rabb and Mac must work from their opposite sides on the court to find out what really occurred the night of the hug.