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.

Admiral Chegwidden welcomes Harm back to JAG by assigning him a tricky case - defending the son of the Secretary of Navy. Harm takes the case when Lt. Nelson, the son of the Secretary of the Navy, is accused by Cmdr. Burke of disobeying an order at sea, an act worthy of a court martial.

The key eyewitness in an attempted rape trial, a decorated Marine corporal, suddenly goes AWOL after he is asked to testify. Harm and Bud follow his trail, and they begin to uncover disturbing facts about the corporal's past that explain why he needs to stay out of the limelight.

When a Navy research project involving psychic phenomena goes awry and results in the death of one of its research subjects, Harm defends the admiral in charge of the project. As Mac prosecutes, she steadfastly proves that the admiral's ESP theories are wrong. But when her friend Chloe disappears and Mac experiences a vision that could save her life, she begins to have second thoughts about the paranormal.

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.

Harm and Mac are sent to Panama to investigate the wife of a Marine officer, Olivia Dunston, suspected of smuggling drugs into the U.S. When faced with the evidence, Olivia feebly denies the allegations, leaving Mac thinking that she's guilty of the charges.

Harm faces a court-martial when a letter critical of the President appears on the Op-Ed page of a newspaper and is traced to his computer. As an investigation threatens Harm's promotion as well as his entire career, a well-known conservative organization offers to represent him and Harm accepts. The key to Harm's defense is to find the actual letter-writer, so Bud digs through Harm's old case files searching for those with an axe to grind.

Lt. Elizabeth ""Skates"" Hawkes, Harm's former RIO (radio intercept officer), comes under fire after the crash landing of a Tomcat aboard the USS Patrick Henry. The ship's captain and Skates' commanding officer both place the entire blame of the crash on her shoulders and press for her court-martial. Barred from the initial investigation because of his relationship with Skates, Harm is finally able to help when he's called upon to defend his friend at her court-martial and employs all of his legal skills to save her military career.

On Christmas Eve, Harm pays his annual visit to the Vietnam Memorial to honor his father who was shot down on Christmas Eve, 1969. At the memorial, Harm meets a beautiful, but mysterious woman, who claims to have known Harm, Sr. She used to be a singer in a traveling USO tour and she met Harm's father shortly before his fateful flight. In an unusual casting twist, Harm stars as his father in this episode, and many familiar faces show up playing different roles.

Harm and Mac stumble upon a miscarriage of justice in a 10-year-old case when they tutor a group of law students in a mock trial. In the original case, an investigation team headed by Admiral Chegwidden concluded that a disgruntled gun captain caused an explosion that killed 29 sailors, including himself. But when the ""defense attorney,"" helped by Mac, and the ""prosecutor,"" helped by Harm, retry the case, a new witness and new evidence are uncovered, prompting Mac and Harm to request that the original hearing be re-evaluated.

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 is trapped below deck on a sinking ship with a sailer, who has been accused of murder, and a guard. Some rescue equipment collapses, blocking the only escape route. As water begins to fill the room, the three men are certain that the situation is hopeless.

At the request of Lt. Cmdr. Brumby, Admiral Chegwidden sends Harm and Bud to Australia to represent a U.S. Naval officer, Kevin Lee, who has suddenly surfaced 28 years after being "murdered" by an Australian sailor. Lee contends that he accidentally killed his Australian nemesis years ago and, in a panic, exchanged identities with the dead man. Now, charged with both deserting and murder, Lee is to be tried in an Australian court, pitting Harm against Brumby. Harm and Brumby are also about to go head-to-head outside the courtroom when Mac appears in Sydney and Brumby decides it's time to make her choose between him and Harm.

The murder/desertion trial of Kevin Lee takes a bad turn after his wife changes her testimony under cross examination. Harm and Mic fights to win over Mac

Harm and Mac are assigned to investigate charges that American GIs shot and killed civilians during the Korean War. They board a plane for Korea, along with a veteran who claims to have participated in the shootings. Korean terrorists take over the plane and insist on punishing those responsible for the alleged war crime.

Harm and Mac face-off in court when a female seaman, charged with desertion, claims she left because her recruiter lied to her about what her duties would be. Meanwhile, Admiral Chegwidden takes the case of an old friend whose impressive career is threatened because of the side effects of Viagra.

Mac prosecutes a SEAL jumpmaster is charged with causing the drowning death of a trainee during a parachute mishap by being hung over and is defended by Bud, assisted by a new female Lieutenant who is very ambitious, wanting to be the first female JAG. Bud & Lt. Singer discovers a safety file that is inadmissible in court that supports the prosecution's contention that the jumpmaster was impaired. The file mysteriously winds up in Mac's car and she thumbs through it. After conferring with Harm who tells her what she already knows, she burns the file. But during questioning court, Lt. Singer objects that Mac is basing her argument based on the file, which Bud reluctantly agrees. Mac is charged with prosecutorial misconduct, removed & replaced by Harm. Having been chewed out by the Admiral, she takes some leave & heads to spend time with Mic in Australia, running into the Admiral & Dr. Walden who are taking their own weekend 'trip'.

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.

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.

Lt. Curtis Rivers (Montel Williams), a Medal of Honor-winning Navy SEAL, is court-martialed for punching a Congressional candidate who falsely claims to be a Navy SEAL. Rivers explains that he is on a crusade to expose Navy SEAL impostors. In order to prove his point to Harm, who is assigned to defend him, Rivers places him in the center of a dangerous plot to expose another false SEAL. Though Rivers assures Harm that his safety is in the hands of two legitimate former SEALS, he finds himself alone in court when Harm misses the trial to pursue a lead on the would-be assassin.

Harm reopens a 10-year-old murder case and unexpectedly incurs the wrath of the victim's daughter, his friend Lt. Cmdr. Teresa Coulter (Trisha Yearwood). Harm feels that the original trial attorney didn't dig deep enough into the case and as he pursues the investigation a new picture begins to develop.

Bud's underachieving brother is accused of making a mistake during a training exercise that nearly killed 15 Marines. But establishing his innocence proves to be a difficult task, thanks to the age-old tension between the Navy and the Marines. Adm. Chegwidden frets over a speech he must give when he is to be given an award. Mic Brumby returns unexpectantly to the States; Mac & everyone are stunned when he announces that he has resigned his Royal Australian Navy commission so that he could move to the USA and be by the "woman he loves."

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.