When Harm and Mac set out to find C.I.A. Agent Clayton Webb's killer after his body is found aboard a burning ship, they inadvertently uncover a rogue government spy agency. Retracing Webb's steps, Harm and Mac learn that he was on a top-secret mission to deliver a high-tech weapons project to the proper authorities when he was stopped. Waiting for Harm and Mac when they discover this, though, is none other than Harm's former nemesis, ex-C.I.A. Agent Clark Palmer, now working with the rogue spy agency, who will stop at nothing -- including Harm's murder -- to get his hands on the top-secret project.

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 is sent to Washington, D.C., to join a committee formed to judge the validity of a shocking television report -- that U.S. forces used sarin gas on fellow Americans during the Gulf War. What he uncovers, though, is so unexpected that he can't present it without testimony from a key witness, Sgt. Morrison, who was actually on the mission in question in the Gulf, but has been missing ever since. Meanwhile, Mac is caught off guard when an old flame, Christopher Ragle suddenly reappears in her life.

Harm and Mac find themselves too close for comfort when they are sent to investigate an international incident on a nuclear submarine. When Harm and Mac, who are already getting on each other's nerves, find themselves in the cramped quarters of the submarine, their relationship is stretched to the absolute limit. Their attempts to stay out of each other's way as much as possible are futile since they must work together to find out why the sub surfaced miles off course, sinking a Norwegian boat in the middle of a regatta. Initially, it seems that the incident was the result of reduced staffing due to a breakout of E-coli. However, as more health problems begin to arise aboard the sub, Harm and Mac suspect a more criminal element than disease.

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.

As Harm considers his future at JAG, he learns that Charlie Lynch -- the ex-Navyman responsible for the murder of Annie, the abused child whose death still haunts Harm -- has resurfaced, placing the little girl's twin sister, Dar-lin, in danger. Putting his career decision on hold until he closes the chapter on Lynch, Harm tracks him to a shipyard where the vicious killer is holding Dar-lin hostage. Overflowing with anger against all Lynch's grisly acts of murder, Harm finds himself in an intense stand-off with him that will leave only one man standing.

Harm and Mac use a party at the Sudanese Embassy as a cover for their investigation of a kidnapping, and they're literally caught by surprise when terrorists take the visiting dignitaries -- and Mac -- hostage. Meanwhile, Bud notices that Harriet seems to be suffering from more than just flu symptoms.

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.

With Harm's eyesight fixed, Harm decides to go ahead and submit a request to be transferred to a fighter squadron. When Lt.Cmdr Parker finds his written request, she is upset at the prospect of Harm being gone for months at a time. Afterwards, Harm goes over to Mac's apartment who has Chloe spending the night with Mac before she is reunited with her real father. Harm informs Mac of the eye surgery and his plans. Mac is equally upset at the prospect of losing Harm. Mic shows up at Mac's apartment after Harm leaves attempting to court Mac's feelings. After Mic leaves, Chloe tells Mac that Brumby and Harm have a crush on her and begins teasing Mac: ""Harm & Mac, sitting in a tree, k-i-s-s-i-n-g."" Admiral Chegwidden passes Harm's request to be transferred onto the SecNav. Not willing to do any favors for Harm, the SecNav is reluctant to intervene.

Harm and Mac's original mission is to represent a Navy flier whose Stealth jet is thought to have crashed in Iran due to a mechanical failure. But when the pilot slips Harm a message indicating that the $80 million plane didn't crash and is hidden, the assignment becomes nearly impossible: get the pilot -- and the costly aircraft -- back to the U.S. without letting the Iranians know that the plane is intact.

Mac's ""little sister"" unexpectantly shows up at JAG headquarters, declaring that she's run away from her abusive stepfather. While she investigates whether Chloe has been abused, Mac has her hands full keeping her from turning the office upside down, then learns that her real father is still alive serving on a ship in the Navy. Despite the cost, Mac convinces the Admiral to allow the two to talk to each other via satellite video-conferencing. Meanwhile, Harm spends the evening interrogating a beautiful Navy doctor arrested for DWI after she lost control of her vehicle on icy roads and ran over a Nativity scene. Harm agrees to defend her when he learns that just before the accident and before she took the breathalyzer test, she had drank some liquid cold medicine (which contains 25% alcohol) Adm. Chegwidden's attempts to fly to Italy to spend Christmas with his daughter, however, with the Washington, DC area mired in snow, most of the flights out have been cancelled.

Harm fears he's losing his mind when he begins to see and hear his deceased father. Worried that he may be going insane, Harm finally confers with his Navy psychiatrist girlfriend who tells him she's treating a Marine officer with similar symptoms and suggests that Harm isn't experiencing anything unusual for someone who's lost a loved one under stressful circumstances. But before Harm can come to terms with the visitations, he begins to suspect that there's something more sinister involved that could cost him more than just his sanity.

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.

After Admiral Chegwiddens daughter, Francesca, is kidnapped in Italy, Chegwidden meets with his ex-wife, Marcella, and her husband, a wealthy Italian businessman, to get more background on Francesca's friends -- and enemies. Chegwidden learns that Francesca was seriously involved with the heir to a Mafia family -- a man Harm and Mac believe is responsible for the theft of Navy missiles for sale to Afghanistan. All intelligence points to the fact that Francesca is caught in the middle of this business deal gone awry, and it's up to Chegwidden and Harm to rescue her from the mob.

Millions of viewers are turned into witnesses when they see a Marine guard shoot an arrested terrorist on live television, and its Harms job to defend him. With Mac on the prosecution, she and Harm are pitted against each other in what seems like an open and shut case of cold-blooded murder. But when Harm is replaced by a civilian attorney with a defense plan that doesnt add up and whose fees are being paid by a wealthy right wing industrialist, Percival Bertram. Harm decides to do some investigating of his own.

When three U.N. peacekeepers are taken hostage in Kosovo, a SEAL team is sent in to rescue them before the end of a 24-hour deadline set by the terrorists. But when heavy ground fog delays the SEAL team by 30 minutes, the hostages are found dead and the team is blamed for their deaths. Mac and Bud begin to defend the team only to have Bud removed because of the defendants' lack of confidence in his legal expertise. Meanwhile, Admiral Chegwidden spends his vacation acting as technical advisor on a movie about the Navy and runs afoul of the Hollywood types who hired him.

Numerous power outages & a ruptured steam line injuring a sailor sends Mac & Harm to the aircraft carrier USS CORAL SEA. While there, they discover two civilian technical representatives onboard and their plan to steal over a million dollars in cash from the Disbursement Office vault; as well as their plan to smuggle it off the carrier. Adm. Chegwiggen helps a former juvenile delinquent who became a decorated SEAL face his leukemia.

Admiral Chegwidden and Clayton Webb make an unlikely team when they join forces to save a C.I.A. agent from Italian terrorists. Webb already tried once unsuccessfully to liberate the C.I.A. agent, who was his mentor, and knows he needs backup in order to retry the mission. He approaches the Admiral, with whom he has a tenuous relationship, but who he knows credits the agent with saving his life in Vietnam. Together, Webb and Chegwidden go to Italy and put into motion a dangerous trap for the terrorists that, if it backfires, will kill all involved. Meanwhile, Harm suffers an identity crisis when his classic Corvette is stolen.

Harm and Mac are assigned to prosecute three sailors charged with the vicious beating of a man they say raped a fellow shipmate. The rape victim, Petty Officer Lopez, tells Mac that, after an evening of drinking with her three male shipmates, she found herself alone at the bar where they ditched her as part of an initiation into their team. The next morning when she awakened in her car, she realized that she had been raped. When the shipmates heard Lopez's story, they exacted revenge on the man they thought attacked her -- the bar owner. But as Harm and Mac wear down the testimony of the three sailors, a very different story about what happened that evening begins to emerge. This episode starts with tying up the loose end of Mac being charged in an Article 32 hearing for perjury (People vs. Mac). She is acquitted, thanks to fancy legal-speak from Harm - although she does not have to face a court-martial, she does end being sent up on an Admiral's Mast, which just might be worse.

When Navy SEAL Medal of Honor winner Lt. Curtis Rivers is fired upon while on a training mission, he returns fire only to discover that he has shot a seemingly unarmed 14-year-old boy. During Harm and Mac's investigation, they discover that the boy may have been accompanied by his uncle, a fugitive wanted by the F.B.I. When Rivers goes AWOL to track down the fugitive and is captured by separatists, Harm and Mac find themselves not just investigating the case, but trying to defend Lt. Rivers in a court that does not recognize the U.S. government and its laws.

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.

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.

Word of her father's imminent death forces Mac to look back at the years of anger and resentment he caused her. She is furious that a priest is trying to convince her to forgive this abusive alcoholic, who was responsible for her own alcoholism. She comes to realize, however, that perhaps her anger had been misdirected all these years when her mother shows up -- after having abandoned Mac many years earlier. Meanwhile, Harm takes a gamble and undergoes laser surgery as a possible cure for his night-blindness.

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.