When skeletal remains are found in a void space on a mothballed carrier, Rabb and Mac must investigate this mysterious occurrence. However, during their investigation, Rabb falls through an unmarked hole in a corridor floor, giving him a concussion. Rabb must find his way out to receive medical treatment. He begins to see the vague shape an Officer who leads him not to safety, but instead to a crew birth which might provide the answer to decadea 's old murder.

In a case where a top female Cobra helicopter has been charged with fraternizing with an enlisted man against orders, Mac must prosecute and Harm must defend. The catch is that the pilot was grounded by the charge while performing her required necessary qualification flights that she must pass to continue flying.

When a Colonel disobeys a direct order to not send his soldiers on a rescue mission in Haiti, things are made worse when a photographer takes a picture that appears to show one of the American soldiers using a child as a human shield, during the fire fight that brakes out during the rescue. Now the SecNav demands that JAG court-martial the Colonel against their advice. Harm and Mac must prosecute, while Chegwidden decides to personally defend the Colonel. However, will Harma 's aggressive search for the truth in Haiti help or hurt his case? Plus, Mac is confronted with prosecuting a fellow military officer she once had a secret past relation with, when she was his subordinate.

When a flight training mission mishap kills a civilian mother and child, after the trailing Tomcat clips a power line, JAG must investigate the cause. The pilot in the leading trainer jet, during the mishap, turns out to be an early mentor of Harma 's. It now turns to Harm to uncover the truth about the accident, even if it means uncovering damaging evidence against his former mentor.

When a crippled Vietnam War vet kills a Vietnamese businessman, Harm must un-wrangle his tell of his killing the Vietnamese Commander of the POW camp he was held prisoner in. He admits to killing the camp Commander as a just act, but wants to also confess to a murder he feels responsible for. But can Harm untangle the web the confessed killer weaves in explain his crime while he was in turned at the POW camp. Things go from bad to worse when the vet tells Harm that Harma 's father was a POW there too. Harm must overcome his disbelief and revulsion in the POWa 's tale, in order to learn the truth of what happened to the POW back at the camp.

When an fully armed F-15 mysteriously disappears during a flight in a storm in the Bermuda Triangle, Harm and Mac are sent to investigate. However, they soon learn the pilot might be part of a terrorist plan to shoot down a commercial airliner carrying an important Palestinian leader. But is the Naval Aviator really in league with this terrorist group? It is up to Harm and Mac to uncover the answer.

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.

After a Navy SEAL, as part of a SEAL team, rescues an American Undersecretary of State, President Clinton nominates him for the Medal of Honor. However, Rabb and Maca 's investigation into the matter leads to disturbing information, such as leaving a man behind, thus breaking the code of the SEALs. To make matters worse, the SEAL in question refuses to help provide any information that would help out his cause.

When a Marine helicopter is struck by an unknown flying object and crashes in the desert killing the Marine pilot, Rabb and Bud are sent to investigate the crash. Soon after arriving at the site and finding some unknown metallic-like fragments near the chopper, they are confronted by men in black from the governmenta 's Defense Security Division (the DSD). They tell Harm they are now in charge of the investigation and to leave the site. However, Rabb doesna 't intend to give up his investigation into this incident so easily.

Rabb, seeking information on his missing POW father, meets with a mob connected Russian. However, during their secret meeting another Russian, a KGB Officer, intervenes, takes the mobstera 's documents, and shoots the mobster. As this is happening, two FBI agents who were tailing the mobster try to enter the scene, but only find Rabb with the gun in his hand after getting it away from the KGB Officer. The KGB officer has disappeared and the FBI agents believe Rabb killed the mobster. Now, the SecNav wants Rabba 's head on a plate. He orders him stand trial for murder. Worse, the lawyer assigned to his case believes he is guilty too, and proceeds with a strategy of mitigation and not for acquittal. Rabb sees that a Brig break is the only way for him to uncover the evidence he needs to clear his name, and to find the KGB Officer (and the information he has on his fathera 's whereabouts). With CIA agent Clayton Webba 's help, he just might succeed.

After a Turkish Colonel assigned to NATO is found dead in a Navy Ensigna 's apartment, Rabb is assigned to investigate. Everything points to the Ensign as having been the object of harassment by the Colonel, but then not all is as it seems. Can Rabb find the truth behind the Colonela 's death? And even if he does, will it even lead to a prosecutable case? Rabb soon leans the truth is even stranger than even he thinks.

When Rabba 's unrequited love-interest, Annie Pendry, comes to him about a situation where she thinks her son, Josh, is lying about seeing a murder, Rabb looks into the sona 's story. As Rabb starts to investigate, an attempt is made on Josha 's life. This leads to a full JAG investigation, which soon uncovers Russian mob connections, CIA investigations, and puts Josha 's life in extreme danger, as the only eyewitness to the real murder he saw.

When a Vice Admiral, who was a former mentor to Adm. Chegwidden, is found dead of an apparent suicide while on a hunting trip, Chegwidden assigns Rabb and Mac to find out what really happened. Even though Rabb and Mac think suicide was the likely cause of death, they soon learn that not all is at it appears to be. Their investigation soon butts head with the other two members of the hunting trip, both of whom have reasons to want the Vice Admiral out of the way, one of which is a high ranking Pentagon Naval Officer. Soon Rabb and Maca 's pursuit leads them in to a deadly encounter which they may not survive.

Rabba 's defense of a Marine tank driver, who accidentally ran over his COa 's tent during a training exercise because he was distracted by his child custody case with his drug using ex-wife, explodes into a hostage situation when the Marine takes his baby and tries to get away in an M1A1 Abrams tank. Rabb must defuse the escalating situation before the tank he has taken does any damage off base.

Rabb must investigate the sinking of a yacht after it was fired upon by a Navy ship trying to interdict drug smugglers. The drug lord owner of the yacht, who has diplomatic immunity, is suing the Navy for the loss of the yacht. However, the investigation takes a strange twist when it leads Rabb and Mac to a group of retired sailors turned vigilantes. Now the JAG team is caught between the ex-sailors and the drug lord, both of whom are seeking revenge.

When the JAG team investigates a sexual harassment charge against a Master Chief, who has had past allegations of harassment, the investigation leads them to a retired Navy Captain with a deep dark secret, which must now be revealed.

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.

Harm begins having flashbacks of his murdered girl friend that he knew from the academy, who looks amazingly like Mac.

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.

Harm gets new evidence, confirmed by an eyewitness, that his father was imprisoned in a Siberian gulag. He travels to Moscow, searching for his father's current whereabouts, when he encounters old adversaries that drive him to steal a MiG.