Il tenente Harmon Rabb e il suo partner, il sottotenente Caitlin "Kate" Pike, indagano a bordo della USS Seahawk dove una donna, pilota di F-14 Tomcat, viene gettata fuori bordo. I membri del JAG devono scoprire chi l'ha uccisa.

Harm viene inviato a bordo di un sottomarino con il suo nuovo partner, il tenente Megan Austin, dove devono evitare che un siluro colpisca una nave civile.

Harm e Meg devono scoprire se il figlio di un ex comandante dei Marine ha ferito alcuni suoi compagni durante un'esercitazione.

Harm e Meg indagano su alcuni omicidi avvenuti al cimitero nazionale di Arlington mentre il passato di Harm torna a perseguitarlo.

Un pilota della marina statunitense piuttosto spericolato muore perché dopo aver intrapreso un volo rovesciato si schianta con il suo aerero dotato di un dispositivo di guida automatica. Nonostante la fama del pilota, suo carissimo amico, Harmon, che sta indagando, contro il parere di tutti sospetta un difetto nell'automatismo e non un errore umano. La situazione si complica quando appare che il defunto avesse una relazione extraconiugale con una collega, rimasta tra l'altro incinta in passato.

Cpl. Parr shoots at an intruder, who he believes shot at him first, at the United States Embassy in Lima, Peru. The intruder, an unarmed 15-year-old teen, is killed. But he wasn't just any boy. He was the brother of Cpl. Parr's girlfriend who (according to her) is pregnant. Harm and Meg are tasked to determine if the teenager was, in fact, unarmed, or if this was an attempt to kill the ambassador. Locations: Lima, Peru

Harm and Meg investigate the theft of stolen missiles at the SEATAC Naval Base. While interrogating PO1 Quinn of the theft, a prison-break takes place and Lt. Austin is taken hostage. Contrary to the Major in charge, Lt. Rabb thinks that this is a well-planned breakout with a big goal. Locations: SEATAC Island Naval Base and surrounding areas

Un marine viene fatto prigioniero in Iraq durante la dittatura di Saddam Hussein per aver sconfinato erroneamente. Viene rinviato a giudizio per spionaggio e su invito dell'Iraq la marina manda come difensori Harm e Mac ad affrontare un processo farsa. In realtà la missione di Harm è recuperare il prigioniero e fuggire con il supporto dei Navy SEAL e l'aiuto di un misterioso e sconosciuto doppiogiochista iracheno

Una recluta marine donna muore impiccata alla corda di un muro di allenamento nel campo di addestramento. Harm si reca sul posto in via ufficiale mentre Meg si traveste da recluta per indagare sotto copertura. Anche se in apparenza sempra un incidente si comprende che si tratta di un suicidio o di un omicidio e i sospetti cadono sulle due istruttrici estremamente severe. Anche il comandante della base ha un atteggiamento omertoso.

Una bambina viene rapita. In apparenza sembrano siano stati degli alieni. La presenza di una base militare abbandonata alimenta il mistero.

During a simulated attack a seriously wounded Marine is found on the beach. JAG is called in to investigate. Harm and Meg follow two ways: An executed Code Red or a brawl. Locations: Camp Pendleton and area; Los Angeles

Harmon Rabb is promoted and his first assignment as Lt. Commander is to defend Capt. 'CAG' Boone in a court-martial. During a mission over Bosnia, one aircraft goes down due to a system malfunction. A Serbian helicopter shoots at the parachuting crew and, to protect them, the CAG shoots down the helicopter. Is CAG, indeed, defending the crew from a hostile helicopter, or is he acting out of revenge, violating a cease-fire, and risking a war? Locations: Bosnia; Naples, Italy; USS Seahawk/Adriatic Sea; Washington D.C.

After a lightning strike, a damaged Tomcat flying over Cuba is forced to land by the Cuban air force. Harm and Meg, accompanied by Cdr. Krennick and undersecretary of state Bair go to Cuba to negotiate the return of the pilot and aircraft. The main goal is to prevent the download of the Tomcat's classified software. But the CIA's actual plans are totally different ... Locations: Washington,D.C.; Cuba

Due to the transposition of two digits of a phone number, Lt. Austin receives a fax with the itinerary for a person with the codename 'Shepherd'. Later, a Commander from the Royal Navy shows up demanding that paper. After receiving it he shoots Meg, seriouly wounding her. Trying to find out who this 'Shepherd' is and why this document is so important, they end up chasing an assassin named 'Hemlock' apparently working for Russian hardliners and trying to kill the man behind 'Shepherd'

- Boris Yeltsin who is due in the US for a secret treaty signing. Locations: Washington, D.C.; Bethesda; Leesburg, Va.

GSgt. Crockett, instructor for snipers at the Boot Camp in Quantico, should be transferred to Bosnia. But there's a deal existing between him and his former commanding officers which says he won't be used in combat missions any longer. After shooting at the colonel 'to get his attention,' he is arrested. Since Crockett once saved Adm. Chegwidden's life, the Admiral orders an investigation to help him. But GSgt. Crockett escapes from the brig and hides in the mountains. Some marines, accompanied by Harm, go out to find Crockett, who's a well-trained and experienced sniper. Locations: Quantico, Va.; Washington D.C.

Il figlio di una senatrice, un pilota di marina muore durante un addestramento con i Navy SEAL. Harm e Meg si trovano a gestire un'indagine difficile tra la madre che grazie al suo potere incalza gli inquirenti, non nascondendo il suo disprezzo per la vita militare e le scelte del figlio, ed i seal che nascondono la verità.

Harm represents the divorced Marine colonel Anderson who has overextended his custody agreement when attempting to spend time with his son before his mother moves him far away. But a warrant goes out to for Anderson, on whom the Vietnam war left its marks. After a local deputy attempts to arrest him without success, a strong police force goes after him. Harm learns what Anderson is really up to and helps him to reach a lodge, the place where he promised to bury an old pal who died back in Vietnam, but was left behind. Locations: Vietnam (1972); California (Tustin, Santa Ana,Big Pine, Bishop)

An evacuation training for a Space Shuttle team ends with a dead pilot caused by a broken cable. Harm and Meg investigate and soon determine that the cable was sabotaged. Harm's first suspect is promoted pilot Lt.Cdr. Lowry. As this is an important mission (repairing a spy satellite monitoring Southwest Asia) it can't be canceled. And since there isn't another eligible pilot, Lowry cannot be removed from the team. A training flight with Lowry and Harm on board has a fatal system malfunction - again sabotage. Lowrey can now be crossed out but the person responsible for these incidents must be found as the scheduled mission must proceed as planned. It is highly possible that there will be another 'unpleasant surprise' to stop this mission. Locations: AFB Vandenberg; Space

On a sailing trip near Hong Kong, Harm is captured by the Chinese military. They want him to reveal the United States' position in case the Chinese should take two islands (which are claimed by Taiwan) by force. To get this information, the Chinese employ various mind games including placing Harm's father in a adjacent cell. Cdr. Krennick and Lt. Austin are offered a deal which includes Harm's freedom and asylum for a Chinese military person. Locations: Hong Kong; Nantou, China

A killed Navy officer working at a destroyer's new defensive system is investigated by Harm with help from Lt. Pike and Cdr. Brockman. Later, during the testing of this system, a malfunction occurs and the system takes over the ship. Without any chance to navigate it, the ship drifts directly to North Korea where the North Korean Navy is already awaiting them. Meg, who came in later, tries with other technicians to break the lockout to regain control over the sabotaged system. Locations: Okinawa, Japan; Japanese Sea

A murdered female lieutenant turns out to be Lt. Schonke, a friend with whom Harm attended Academy, but neither Cdr. Krennick nor Agent Turque, an abrasive civilian investigator, buys Harm's claim that his relationship was strictly platonic. After the primary suspect of the murder is also found dead - a more than dubious suicide - Harm finds himself being the number one suspect for both murders ... Locations: US Naval Base Norfolk, Va.; Washington D.C.