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 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.

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.

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.

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 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.

While Harm is sent to Russia to help the Russians find a better way to implement their military justice procedures, Mac and Bud remain behind to prosecute a Naval commander charged with selling military secrets to the Russians. Once in Russia, Harm becomes involved in investigating high level corruption in the military.

Meanwhile, Mac is on the verge of making a deal with the traitorous Naval officer when he and his lawyer are murdered. Mac and Webb then discover that the traitor was linked to a Russian assassination plot. But Mac's attempts to alert Harm fail, and he is caught in an ambush with a Russian who reveals the life-changing secret to him.

At Christmas time, while everyone else at JAG is enjoying the happy time of the season, Bud & Harriet are at little Sarah's gravesite unveiling her headstone that has just been placed. Bud vows that it just can't end like this and insists on finding out what happened. Bud & Harriet approach Mic to have him represent the Roberts in their case against Dr. Gettis. Mic warns Bud to stop, leading Bud to realize that Mic can't represent them, as his practice is representing Dr. Gettis. Harriet tries to talk Bud out of pursuing the case, but her pleas are ignored by Bud.

Mac is assigned the case by the Admiral despite Bud's plea to be the lead attorney. Even though he is ordered to stay away from the case, he nonetheless can't. Mac questions Dr. Gettis as to why he took so long to respond when Harriet labor was in trouble. Dr. Gettis claims that his pager battery had died & didn't realize he was needed until he heard the overhead page for him.

Harm's friendship with Capt. Volkonov puts him in a precarious position when a Russian submarine blows up and the Russians claim that a U.S. submarine was responsible. It's up to Harm to convince his friend (& the world) that the accident was caused by a faulty new Russian torpedo, without divulging highly classified material.

Meanwhile, Mac is sent onboard the USS Watertown to observe when the Congressional committee headed by Rep. Latham investigates as to why women are not allowed to serve aboard submarines.

Renee & Mic are left behind wondering whether their really is something between Harm & Mac.

Harm and Mac investigate the Osprey, a controversial Marine Corps helicopter/airplane, after one almost crashes with Congresswoman Bobbi Latham on board.

Harm and Mac investigate a Marine general claims that a Navy doctor caused the death of his teenage daughter during routine surgery.

Meanwhile, Bud is so frustrated with the simple cases he's been given, he decides to investigate what appears to be an open and shut case and gets surprising results.