A band of rogue patriots hijack the Declaration of Independence during a transfer. Maj. Sarah MacKenzie and Ltjg. Bud Roberts join the JAG gang; they and Harm investigate. They find the thieves, make a deal, then defend the leader in court.
An enlisted Marine escapes from a Navy brig; he takes the admiral, Bud, and Sarah as hostages. At his direction they conduct a mock trial, retrying the same matter. Bud judges, Mac prosecutes, and the admiral defends, as he did originally.
An F-14 Tomcat crashes into the sea after a major engine failure; the squadron has a reputation for having become jinxed. Harm, Sarah, and Bud investigate. Harm again flies a Tomcat; he helps a fellow aviator, and he disproves the jinx.
A SEAL dies of gunfire during a mission; the government charges the CPO in charge with the murder of his best friend. Harm prosecutes, and he deduces how and why the death took place; he then tells the court that he cannot prove his case.
A woman Naval aviator accuses the CAG of sexual harassment after he grounds her. Harm, Mac, and Bud investigate; a congresswoman intervenes. The CAG says that the pilot is substandard. The tragic climax shows who's right. Bud meets Harriet.
Intruders enter the US submarine facility at Holy Loch, Scotland, then kidnap the baby son of a single woman Naval officer. The father is a member of the IRA. Harm and Mac provide help in Belfast; amid fireworks and deception they succeed.
While the admiral and his girlfriend jog together, they encounter a prankish booby trap; then Bud brokers a deal about a goat and a midshipman. Later A.J.'s lady dies in a real explosion at his house; he, the gang, and Webb work it out.
While Harm gives Mac a ride in his antique biplane, the engine quits, so they land in a woodsy area. Poachers nearby kill a game warden; Harm and Mac meet them. One poacher opens fire on them, and they escape, but they meet difficulties.
The King of Romania and his daughter visit Washington. Communist extremists oppose the king, and they threaten to assassinate the princess. The SecNav appoints Harm to escort her. The antagonists try but fail. Harriet shows up in DC.
An enlisted Marine dies during a covert operation against the home of a drug lord in Colombia; his recon team leaves his body behind. The admiral sends Harm, Mac, and Bud to Colombia to investigate; he implies that he also expects them to return the body to the US. Webb is involved in Colombia (even more so than he prefers). The Three Musketeers encounter much intrigue and deception, so they respond in kind. Harm cons the conners, and a double agent becomes a triple agent. The JAG team wins, so they take back with them not only both the dead Marine and Webb but also ...
Two Marines sustain injuries during a training exercise. Mac and Bud investigate whether the company commander has placed his men at undue risk. Harm goes undercover. A third Marine becomes injured. The captain confesses.
Three thugs try to rob a C store, but a homeless former SEAL intervenes and kills them; he runs into a nearby church while Bud prays there. A standoff develops and resolves; Harm successfully defends the SEAL in a civilian criminal court.
A car hits Harm; Mac takes him to a hospital, where an Israeli official undergoes a heart transplant. Members of the Hamas seize control of two floors, to hold the official as a hostage for a prisoner exchange. Harm and Mac help.
Harm, Mac, and Bud observe war games in the Black Sea, Mac aboard a US ship, Harm and Bud aboard a Russian ship. The two skippers, old enemies, try hard to settle grudges; the Russian, a psychotic, goes too far. Harm and Bud reach safety.
An ensign dies while with the wife of a chief petty officer; the chief faces a charge of murder. Harm prosecutes, and Mac and Bud defend. Evidence comes from an unexpected source, and justice prevails. Bud and Harriet spend time together.
Aboard a decommissioned Naval vessel, inspectors discover the skeleton of a missing aviator. Harm and Mac investigate. Harm finds an important book, which contains a clue about the whereabouts of his father, but the book disappears.
A single woman Marine helo pilot, an officer, faces charges for disobedience and an adulterous relationship with a married enlisted man. Mac and Bud prosecute, and Harm defends. Rep. Bobbi Latham attends, to ensure equal treatment.
A Marine recon team extracts other Marines imprisoned in Haiti due to rebel action; civilian deaths result. The officer in tactical command stands accused of disobeying an order to wait. Harm and Mac prosecute; the admiral and Bud defend.
An F-14 Tomcat clips the top of a utility tower. The aviators eject, but the aircraft crashes and kills two people on the ground. The evidence implicates the squadron CO, a mentor of Harm, who investigates and prosecutes. Mac defends.
A paraplegic Marine veteran kills a Vietnamese man in Georgetown, then he goes to the JAG headquarters and confesses. The victim was the cruel commandant of the vet's PoW camp. Harm volunteers to represent the vet in the civilian court.
Inside the Bermuda triangle an armed F-14 Tomcat vanishes. The pilot's wife and daughter suddenly disappear from family housing at NAS Jax. Harm, Mac, Bud, and even the admiral investigate; they figure it out, and the Navy makes it right.
A carrier-based F/A-18 Hornet accidentally fires a missile and destroys an aircraft first described as a North Korean commercial liner. Harm, Mac, and Bud investigate; they discover not only the cause but also a spy message and the spy.
A SEAL team rescues a captive US diplomat in Lebanon; the PotUS wants the OiC of the team to receive the Medal of Honor. Harm, Mac, and Bud investigate, but they have trouble in learning anything because nobody talks; Harm figures it out.
A Marine Corps helo has a midair collision with an unknown aircraft; all but the pilot survive. Harm and Bud investigate. People from a mysterious agency take control of the site, and Harm locks horns with them, but he solves the mystery.
Harm tries to buy stolen documents allegedly about his father in Russia, then Harm faces a charge of murder. Webb helps Harm. The matter goes to a pretrial hearing; Mac represents Harm. Afterward Mac suddenly again speaks with the admiral.
A woman Navy ensign shoots and kills a Turkish colonel; she claims self-defense. Harm, Mac, and Bud investigate, and Harm defends her in a preliminary hearing. Later the admiral tells Harm more. Bud and Harriet take another step together.