Uno scheletro viene trovato a bordo di una nave della marina che sta per essere smantellata e Harm è convinto che questo sia legato a suo padre disperso in azione in Vietnam.

Una pilota dei Marine è accusata di adulterio e disobbedienza a un ordine diretto e Harm la difende al processo mentre un membro del congresso interferisce nel caso.

Un tenente colonnello dei Marine è accusato di disobbedienza per aver inviato dei soldati a salvare altri marine prigionieri ad Haiti. Il caso è seguito dal presidente a causa dell'eco provocata per l'uccisione di civili durante l'operazione. Harm deve accusare il militare, Mac deve difenderlo.

Harm risks ending the career of his mentor, as well as their friendship, when he investigates a training accident that killed two civilians.

When an F-15 has a mid-air accident and the occupants are forced to eject, a mother and her child are killed on the ground by the falling debris. Mac is assigned to represent the pilot as Harm investigates the cause of the accident and the leader of the training mission, Capt. Hachausen, his former flight instructor and mentor. When Harm's probe reveals that the captain's been covering up problems with his eyesight and the pilot of the plane is covering up for the captain, Harm must decide whether to reveal his findings -- information that would certainly end his mentor's career.

When a former Vietnam POW arrives at JAG headquarters to report a murder he's just committed, Harm confronts a very complex individual who may know something about his MIA father.

When Willie relates the fact that he was imprisoned with Harm's father and then blindsides Harm by claiming that his father was a turncoat, the information has a profound effect on the JAG lawyer. Willie, a very complex individual, has been waiting 30 years to tell his story in his own way. Ultimately, Harm finds out that Willie's murder victim was the contemptible, sadistic commander of the POW camp where Willie had been -- but that's just the beginning of Willie's incredibly sad war story.

When a fully armed and piloted Navy F-14 disappears during a storm, the JAG team is called in to investigate all possible scenarios, from pilot suicide and terrorism to the curse of the Bermuda Triangle and UFO interference.

When the plane's co-pilot surfaces, bloodied and disoriented, Harm and Mac get some new information that steers them away from Twilight Zone explanations and instead points them in the direction of kidnapping, terrorism and a hard-core militia group's plot to assassinate a PLO delegation heading for Washington by using the pilot -- and his plane -- to do the dirty work.

International tensions mount as Harm, Mac and Bud board an aircraft carrier in the Sea of Japan to investigate the accidental shooting down of a North Korean civilian airline by Navy jets.

While negligence on the part of the Navy fliers is indicated, Harm and Mac uncover evidence of a spy aboard the carrier. Meanwhile, the threat of war becomes real when a U.S. salvage vessel is sent to the site to help with the investigation and two North Korean warships threaten to sink it if both U.S. ships don't leave the area immediately.

Un elicottero dei marines precipita senza apparente motivo. Rabb viene inviato ad indagare, con Bud, e scopre che l'elicottero è stato abbattuto da un veivolo segreto. Mac lascia il Jag.

Rabb cerca di acquistare un dossier sul padre da un russo; questi viene ucciso da un misterioso compatriota che scompare. Rabb viene imprigionato per omicidio ed è costretto a evadere, per scagionarsi, con l'aiuto di Clayton Webb, che lo vuole usare come esca per catturare l'ex colonnello russo, adesso spia indipendente e vero omicida dell'ucciso.

Harm affronta la difesa impossibile di una donna ufficiale che, senza testimoni, aveva ucciso un diplomatico straniero disarmato, e che dichiara di averlo fatto per legittima difesa, avendo semplicemente intuito che il diplomatico voleva aggredirla. Harm contro le aspettative di tutti riesce a discolparla ma le cose non sono affatto quello che sembrano.

Annie Pendry, a widow, comes to Harm for help after her young son, Josh, witnessed a murder while on a class trip to Andrews Air Force Base. After Harm and Josh are the targets of a drive-by shooting, Harm moves Josh and Annie into his apartment -- and into his life. Harm discovers that the original crime and the drive-by shooting are tied to a ruthless international arms dealer, but not before Josh is kidnapped by the dealer in order to silence him as a witness.

Admiral Chegwidden investigates the apparent suicide of his mentor, Admiral Clancy, who allegedly shot himself while on a hunting trip with several friends. Chegwidden can't believe that his friend would kill himself, and discovers that someone else may have actually pulled the trigger.

Due to frustration at being unable to wrest custody of his son from his drug addicted wife, Corporal Wetzel was distracted during a war game exercise and crashed a tank. Accused of dereliction of duty, Wetzel admits to being diverted on the job, but insists that Mac and Harm must keep him out of jail, since his arrest would certainly mean losing his son.

Harm and Mac like Wetzel and understand that his frustration accounts for his poor judgment. But nobody's more surprised than they when Wetzel winds up in a tank in a stand-off with the military, questioning why he's being forced to choose between being a marine and being a father.

When a luxury yacht owned by a reputed South American drug trafficker mysteriously sinks and the Navy is suspect, Harm, Mac and Bud are put on the case. Meanwhile, Artemus Sullivan, a World War II Navy veteran, with the help of his aged cronies, devises plans from a nursing home to make sure the drug dealer responsible for Sullivan's grandson's death is brought to justice. But when Sullivan is kidnapped by the drug dealers, his mettle is tested, as is that of Harm and his team as they race to rescue the war hero.

Harm, Mac, and Bud investigate claims of sexual harassment aboard an aircraft carrier. Mac's boyfriend, Dalton Lowne, is the defendant's attorney, and Mac is shocked when she discovers that he has been copying information from her files.

In order to solve the case, and combat Lowne's dirty tricks, Harm enlists the aid of Congresswoman Bobbi Latham. Justice is served, though many people's lives are changes as the result of Lowne's tactics.

Following her ugly break-up with Dalton Lowne, Mac has reason to believe that he's stalking her -- until he's killed during an apparent car-jacking and the stalking continues. Much to Harm's dismay, the strain of the two events pushes Mac to the edge -- and to the bottle. Concerned for Mac's safety and sobriety, Harm intensifies his search for Mac's tormentor before he causes her bodily harm.

When Harm takes young Josh on a weekend cruise for Navy families aboard the frigate, pleasure turns to fear when the ship is taken over by terrorists who intend to fire missiles at Cuba. After Josh and Harm manage to elude the terrorists, they try to contact authorities about the situation. But the plan goes awry when Harm is found out, and he then tries to strike a deal with the terrorists while also racing to foil the plot before the innocent civilians get hurt.

Vengono spiegati gli avvenimenti successivi all'ultimo episodio della prima stagione che si chiude con un cliffhanger. Harm ha scoperto l'assassino di Diane, sosia di Mac, donna cui ricambiava un sentimento forte ma inespresso e per il quale avevano deciso di parlare di un "futuro comune". Harm vuole vendicarla quando viene scoperto da Mac e le racconta tutto per poi scappare via. Trova l'assassino e gli punta addosso una pistola, dicendogli che non vuole portarlo al processo, quando sopraggiunge Mac in uniforme da guardiamarina. L'assassino la scambia per il fantasma di Diane e terrorrizato cade in mare, muorendo prima che Harm si possa vendicare. Alla fine Harm, guardando Mac, la bacia sulla bocca per la prima volta; lei accetta però poi gli dice che lo sapeva che lui stava baciando Diane e non lei.

Clark Palmer, a renegade government agent, breaks into Harm's apartment and incapacitates him. Palmer then makes a cast of Harm's face in order to prepare a mask that he can wear to pass for Harm. Palmer plans to murder the key witness in the trial at which Harm and Mac are currently prosecutors.

When Harm doesn't show up for the start of the trial, Mac takes his place, leaving Bud to search for the missing JAG lawyer. When Bud finds Harm trapped in an ingeniously booby-trapped apartment, the two must find a way to escape before the assassin can carry out his plan.

Members of the JAG team encounter resistance from Navajo tribal elders when they insist on DNA testing to verify that human remains are those of heroic Navajo ""code-talker"" Jimmy Blackhorse, who has been missing since World War II. Forensic pathologist Lt. Cmdr. Teresa Coulter joins Harm and Mac on the case.

The Navajo elders consider it a sacrilege to tamper with the remains of the dead and, furthermore, the Navajo medicine woman is certain that the remains do not belong to the esteemed Blackhorse. While the veracity of scientific evidence is argued against that of tribal custom and the metaphysical, Teresa finds herself falling for Harm and putting the entire assignment in jeopardy.

Political pressures come into play after an F-14 pilot clips a ski helicopter during a NATO exercise over Italian airspace, killing six civilians. Harm and Mac are assigned to opposite sides in the case, but the Italian government wants to prosecute on its own.

Bud has his hands full when his obnoxious and abusive father, Big Bud, and his younger brother, Mikey, arrive in town for his wedding. Big Bud throws a stag party at a boisterous strip club where Harm's dress whites end up on the body of a stripper. A fight breaks out and Harm, Bud and Chegwidden find themselves in the slammer on the day of the wedding.

While Mac goes downtown to bail them out, Harriet begins to have second thoughts about the imminent nuptials.

(The time is 1980, several Russian soldiers are guarding a prisoner who is Harmon Rabb, Sr. at a train station. The KGB take a photo of the persons gathered there - a photo which has made its way to Harmon Rabb, Jr. in the present time.)

Clayton Webb meets with Harm at JAG and tells him who the men in the photo are. Webb mentions that one of them, Victor Lushov is now working in San Diego. Harm requests from the Admiral to take an F-14 hop to San Diego to visit his mother, keeping secret his true intentions.

In San Diego, Harm meets with Lushov who turns out to be a Russian pilot who was instrumental interoggating Harm, Sr. after he was shot down over Vietnam, later befriending him. He tells Harm Jr. all about what happened to his father, that Harm Sr. fed all kinds of disinformation to the Russians, which was worse than telling them nothing. Lushov gives Harm Jr. the KGB file number for his father. And says he wants to live and will not repeat what he has said to anyone.