Harm and Mac face off on opposite sides of the courtroom at the trial of a Navy Seal accused of murdering his closest friend during a mission against terrorists.

Despite evidence to the contrary and the accused's unwillingness to cooperate, Mac, who is defending him, feels there's more to the story than meets the eye. Her fervor causes Harm, who is prosecuting the case, to dig deeper into the dead boy's personal life. It is Harm who discovers that it isn't a case of murder -- but, in fact, the victim begged his friend to kill him in order to keep a secret from his father, a strict former Navy petty officer.

Harm and Mac investigate a female fighter pilot's charge of sexual harassment against her commanding officer.

The pilot, Lt. Marilyn Isaaks, claims to have been grounded for pressing charges of sexual harassment against her commanding officer, Capt. Boone (guest star Terry O'Quinn). Capt. Boone claims he grounded her because she's a bad pilot. While Harm and Mac are called in to conduct a thorough investigation into the allegations, congressional intervention forces Boone to schedule Isaaks for a training flight -- an action that Harm feels will have deadly consequences.

Hospitalized with a knee injury, Harm is forced to take action when the Hamas, a terrorist Islamic Resistance group, takes the hospital hostage.

An Israeli diplomat undergoing a heart transplant provides the Hamas terrorists with the perfect negotiating tool. They take over the operating room -- as well as the entire hospital -- and use the diplomat as leverage while demanding the release of one of their imprisoned leaders. Meanwhile, Mac is trapped in the hospital cafeteria trying to negotiate with two terrorists.

Harm, Mac and Bud are assigned sea duty to be official observers during a joint war games exercise between U.S. and Russian naval forces, but the games take a deadly turn when the rival captains decide to make the battle real -- and Harm, Mac and Bud are trapped on board the warring ships.

The captains are bitter enemies from Cold War days and have deemed this their final grudge match. Both are determined to make it a battle to the death, even if it means going down with their ships -- and taking everyone on board with them -- and it's up to Harm and Bud to defuse what could become World War III.

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 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'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.

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.

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.

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.

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.

Having been shot at by Russian fighters, Mac & Harm are forced to eject from their plane, which then noses into the bottom of a very deep lake. The Russians announce to the world that Harm & Mac have been killed, which is broadcasted back to the USA by ZNN reporter Chuck DePalma.

Webb tries to convince the Admiral that they have been killed, but when A.J. learns their bodies haven't been found, A.J. becomes irate and vows to go to Moscow himself to look for them. The SecNav orders A.J. not to go, who replies that the SecNav doesn't want to try & stop him.

In Russia, A.J. meets with DePalma who tells A.J. that he doesn't believe the Russians, that certain things in their story don't add up.

In the woods, a husband & wife gypsies come across Harm & Mac. They are disappointed when they learn that Harm & Mac are not American Spies as at least the spies have gold coins to give to Russians that help them.

Harm and Mac must don their diplomatic hats when they're dispatched to Tokyo to represent an ensign accused of raping a young Japanese girl. Once the trial begins, the disparities between Japanese and American courtroom procedures put Harm at odds with the ensign's Japanese defense attorney, in turn putting US/Japanese relations at an all-time low.

When what began as the trial of an ensign turns into a trial of the United States Navy, Harm and Mac realize that in order to defend the ensign from life in a Japanese prison, they must actually solve the rape case on foreign soil.

Harm volunteers to defend a psychotic Vietnam vet accused of aiding the suicide of a fellow V.A. patient. While Harm argues in court that Roscoe Martin withheld the victims medication as a way to free him from the trancelike state in which it left him, the prosecution claims that the lack of medication is exactly what caused the mans death. Disappointed with the direction of the case, Roscoe feels that the cards are stacked against him and engineers an escape from the V.A. facility with three other patients. Their escape takes them to Harms apartment, and a negotiable situation turns deadly when guns are drawn and a SWAT team swoops in to help with what it sees as a hostage situation.

When a fighter pilot claims he heard the voice of God tell him not to fire on an attacking Iraqi, Harm and Mac are sent in to investigate his claim. Despite the pilot's assertions that he heard God, Harm insists on finding a more ""military"" explanation. When Harm fails from the ground to discover the origination of the voice, he suggests that Rice duplicate his earlier mission to see what they can learn about the incident in the sky.

Mac is arrested and placed on trial for a major felony, along with her former commanding officer and mentor, Col. John Farrow. Conviction could result in long prison terms.

Harm volunteers to defend her, but his efforts are thwarted by Farrow's defense attorney, JAG exchange officer, Australian Navy Commander Mic Brumby. Harm feels that neither defendant has come clean with the truth and he begins to search for evidence which is not forthcoming from either one. Ultimately, he learns that Mac and Farrow have each been trying to protect the other. The key witness in the case turns out to be a major surprise to both defendants.

When Harm views the body of the severely neglected, abused and abandoned young girl, he unexpectedly becomes emotionally involved and decides to call in the help of Teresa Coulter to help him identify the child and find her killer.

After Teresa performs her own autopsy, she uncovers some clues to the girl's history that lead her, along with Harm and Mac, to the last place the child lived -- as well as to a recently released convicted child molester.

Bud's first case as a newly sworn in JAG attorney is to defend his father, a retired Navy Chief who's been accused of having been involved in defrauding the Navy when he was in charge of Ship's Stores. Though the two have been estranged, Bud feels a strong obligation to his father, who specifically requested him to be his attorney. Harm is the designated prosecutor, which spooks Bud, as he knows he's going up against the best.

As lowest ranking lawyer at JAG, Bud is assigned to accompany Raglan, a former special Forces operative who is hired by the Pentagon to test security at military bases. Raglan's current mission is to test the security around a U.S. nuclear attack submarine. But when Raglan goes too far and hijacks the sub with Bud on board, Harm is called in to chase the sub down by second guessing his old friend. The cat and mouse game becomes deadly, though, when it appears that Raglan has switched sides, demanding millions of dollars in ransom or he'll take aim on a U.S. target.

Mac is assigned the personally distasteful task of representing a fellow Marine who is appealing his death sentence for the murder of three other Marines. She believes that the defendant, Kenneth Farmer, should receive the death penalty, but she must argue otherwise in court. Brumby, who doesn't believe in capital punishment, must argue in favor of it.

However, in attempting to overturn the original guilty verdict, Mac must argue inadequate counsel by the corporal's previous lawyer: then-Commander A.J. Chegwiggen. The appeals court lets stand the original guilty verdict, but orders a new sentencing hearing.

Mic is recalled by the Royal Australian Navy and must leave within 72 hours. As a result, Harm is assigned to replace Brumby at the new sentencing hearing. Despite Mac's arguments to the defense of Corporal Farmer that was not raised by then-Commander Chegwiggen, Corporal Farmer is again sentenced to death.

Admiral Chegwiggen throws a goodbye party for Mic at the local bar.

Harm and Chegwidden fight an attempt by a salvage hunter to excavate the remains of a submarine that disappeared in 1941, just before the attack of Pearl Harbor. Meanwhile, Bud takes on the heavy burden of trying to keep an obese petty officer from being discharged for failing to lose weight.

Mac goes undercover to help Harm investigate charges of sexual misconduct against Chief Petty Officer Merker who is the leader of the Wiccans, a local witches coven with many Navy members. The female seaman who brought the charges claims she was seduced when she fell under the man's spell, but Merker claims the sex was consensual. The Wiccan's attorney is sharp and claims his client is the unfortunate victim. However, Mac learns that another young woman suffered the same fate. He convinces her to testify and Merker is found guilty.

Later, Mac learns that Mic Brumby was also thrown into a compromising position while undercover in the Royal Australian Navy.