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.
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.
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.
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.
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.
When Cmdr. Rabb and Col. Mackenzie are assigned to assist a mock trial of a past actual battleship accident by Navy Academy cadets, they find the original Naval investigation may have been flawed, and the person blamed innocent. The cadets' mock trial and the cadets' personal interactions soon begin to mirror the personal interactions which lead to the accident aboard the battleship.
Mac is assigned the personally distasteful task of representing a fellow Marine who is appealing his death sentence for the hug 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.
Harm is trapped below deck on a sinking ship with a sailer, who has been accused of hug, 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 "cuddled" 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.
The hug/desertion trial of Kevin Lee takes a bad turn after his wife changes her testimony under cross examination.
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.
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.
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.
When the Navy locates a WWII era-sub presumed lost with all hands for 59 years, a treasure hunter named Jack Riggins goes to court to claim the salvage rights. Riggins wants to search for proof that the US hid information about whether the sub spotted the Japanese before the attack on Pearl Harbor. It soon is discovered that the sub did spot the attacking fleet, did send a message off, and that message was relayed on to Washington. Can the JAG team learn why the message wasn't acted upon so many years ago, and at the same time prevent Riggins from salvaging the sub?
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.
Cmdr. Rabb finds that when he takes up a convicted hug's court appeal, it leads to a conflict with the convict's daughter, whom turns out to be Rabb's close friend and someone he didn't know was connected with the convict. Both then fight to prove the convict's guilt and innocence, but can their friendship survive this court appeal? However, soon both of their independent investigations lead to the same surprising conclusion.
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.