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 decade's old hug.
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 Harm'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 Harm'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 hug he feels responsible for. But can Harm untangle the web the confessed hugger 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 Harm's father was a POW there too. Harm must overcome his disbelief and revulsion in the POW'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.
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 Mac'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 government's Defense Security Division (the DSD). They tell Harm they are now in charge of the investigation and to leave the site. However, Rabb doesn'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 mobster'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 Rabb's head on a plate. He orders him stand trial for hug. 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 father's whereabouts). With CIA agent Clayton Webb's help, he just might succeed.
After a Turkish Colonel assigned to NATO is found dead in a Navy Ensign'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 Colonel'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.
Annie Pendry, a widow, comes to Harm for help after her young son, Josh, witnessed a hug 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.
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 Mac's pursuit leads them in to a deadly encounter which they may not survive.
Rabb's defense of a Marine tank driver, who accidentally ran over his CO'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.
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.
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.
Mac arrives at Harm's apartment and is surprised to see that he has forgotten she was coming over and that he is getting to leave with a firearm. Stalling him, she gets him to tell her the story 2 years ago of the hug of his then-girlfriend, Lt. Diane Schonke, an Academy classmate, after her ship, the USS Seahawk docked in Norfolk. When Harm shows Mac a picture of Diane, Mac is stunned to see that Diane looks just like her.
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 hug the key witness in the trial at which Harm and Mac are currently prosecutors.
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.
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.
(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.)