Trouble in the JAG office starts when Gunnery Sgt. Victor Galindez, ""Gunny,"" is charged with assault following an off-duty altercation outside a gay bar. It comes to light that P.O. Tiner was also involved in the brawl, having come to the aid of his companion, whom Gunny was roughing up. Meanwhile, Mac finds herself wrestling with the ""don't ask, don't tell"" policy as attitudes toward Tiner change around the office under suspicions that he's gay.

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.

Harm discovers evidence that his father, an MIA from the Vietnam War, may be alive and under KGB control in Russia. Harm and Mac are investigating the murder of a Navy pilot whose body was found hidden aboard the decommissioned aircraft carrier the USS Hornet. With help from a local police lieutenant, they discover a motive for the crime, which involves a list of MIAs and POWs supposedly still alive and under KGB control in Russia -- and the list includes Harm's father. But before Harm can act on the information, the book mysteriously disappears along with the helpful police lieutenant.

A top female helicopter pilot is accused of disobeying an order---to cease her affair with a married enlisted man, and a Congresswoman is determined to ensure the pilot's fair treatment as a potential court-martial looms.

When a Marine colonel defies orders from superiors, as well as the State Department, and rescues his men who are being held and tortured by a Haitian warlord, he is court-martialed. Harm and Mac are assigned as prosecutors and are shocked when they find they must go head-to-head with Chegwidden. Bud was put in a position to choose which side to go on. He choosed Admiral Chegwidden

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.

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.

When Harm, Mac and Bud are ordered to run a routine background check on a Navy SEAL who is a candidate for the Medal of Honor, they uncover unsavory information that may make him unworthy. Lt. Rivers is up for a medal after he single-handedly rescues the undersecretary of state from fundamentalist terrorists. Harm and Mac, in their investigation, find Rivers, an African-American, to be a very tough, complex and uncommunicative individual who is totally devoted to his country and his duty. But his men paint a different picture of him as a gung-ho loner who doesn't care about the safety of his team and, in fact, botched the mission by leaving one of his men behind. Rivers finally agrees to open up to Harm -- but only if Harm can withstand arduous SEAL training for one day -- including the brutal manhandling required of the ""hostage interrogation.""

Harm & Bud are sent to Twenty-nine Palms Marine Base to investigate the mid-air collision of 2 helicopters & subsequent crash of one helicopter which killed the pilot. Upon arrival at the crash site, they learn that the ""other"" aircraft was not another helicopter as was first thought. A piece of wreckage that is found that belongs to the ""other"" aircraft only deepens the mystery. When members of the Defense Security Division appear onscene with orders to take over the investigation and crash site, Harm becomes convinced that a major cover-up is in the works. The base commander, Col. Barrett gives Harm time to investigate further. When Harm & Bud are out driving the base at night, they see an unknown type aircraft flying above them and follows it, but are soon blocked by a fence over the road marking the property of the ""Bradenhurst Corporation"".

Harm meets with a Russian 'contact' in order to purchase documents that will prove his father was taken to Russia after being shot down in Vietnam. However, during the transaction, they are interrupted by a KGB agent, Col. Parlovsky who shoots & kills the Russian, then runs off as FBI agents show up, finding Harm over the body, with the gun & documents he wrestled away. As the FBI wants to hold him for the murder of the Russian, Adm. Chegwiggen manages to have Harm transferred to a military brig, and court-martialed, much to the dismay of the FBI agents. CIA agent Clayton Webb, knowing that it was Parlovsky, not Harm that committed the shooting, arranges for Harm to escape from custody in hopes Parlovsky will contact Harm. In the end, Parlovsky makes contact with Harm, but they both get away before Webb can catch them. Parlovsky tells Harm the documents were a fake and burns them. He then leaves, refusing to help clear Harm of the shooting.

Harm's skills as a lawyer are challenged when he defends a female ensign who claims she murdered an officer because her ""instincts"" told her he meant to hurt her. The ensign claims that when the officer entered her apartment on false pretenses, she felt threatened by him and killed in self-defense. Though the defense is decidedly thin -- no weapon was even found on the man's body -- Mac and Harm decide to stick with the case and are determined to help the ensign remember forgotten details of the event.

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.

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.

(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.

While patrolling the Mediterranean near Yugoslavia and against the orders of Harm, his division commander, Lt. Buxton fires on what he believes is a Serbian armored car about to attack Kosovar refugees. As Buxton and his pals are celebrating his victory back aboard the aircraft carrier, however, the grave news arrives: those ""Serbs"" Buxton attacked and killed were, in fact, Russian peacekeepers, and Buxton made the mistake while under Harm's command. Mac prosecutes what appears to be an open-and-shut case of a Marine weapons expert accused of reckless endangerment.

Unexpectedly, the wily Buxton demands that Harm and Brumby be his lawyers, thereby preventing Harm from testifying against him and forcing the two adversarial lawyers to work together. The contentious trial continues with Mac and Roberts prosecuting, and the pressure is enormous as the U.S. Navy and the Russian government vigilantly follow the trial to ensure that its own agendas are met. Meanwhile, the Navy has its own special plans for the troublesome Buxton.

Harms fitness report is coming up and the realization that maybe it really is too late to be a fighter pilot. During a dangerous mission over hostile Serbian territory, Harm's wingman's plane is shot up and Harm performs top-gun maneuvers to keep the disabled plane aloft until it's over friendly territory. Meanwhile, with a new Gunny in the office, Bud & Tiner fall over themselves as they compete against each other in an online auction to purchase tickets to a concert, in order to impress the Admiral. They end up looking foolish when it is discovered that the Gunny got the same tickets for free.