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.

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.

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.

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.

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.

Harm is distraught when his newly discovered half-brother, Sergei, is framed for a crime punishable by death, while Mac arrives in Russia to prevent a presidential assassination.

Harm & Mac defend Adm. Boone in court against the charges that he was responsible for massacrering civilians. Although he is eventually acquitted, he decides that it is probably best to retire from the service, despite Harm's objection that the Navy need men like him.

Harm and Mac travel to Bahrain to determine if a female Marine found aboard a terrorist boat that attacked a U.S. Naval destroyer was coerced into helping her captors or was a willing participant.

Sgt. Joan Steele, kidnapped by terrorists a month before the attack, insists that the cooperation she gave the terrorists was designed to foil their plot. Harm, who is defending her, finds her claim dubious. CIA Operative Clayton Webb asks for her help in tracking down a known terrorist who is planning to bomb another U.S. target within 48 hours, and Steele readily agrees. But then she suddenly disappears, confirming Harm's suspicions and, more importantly, leaving the target -- a busload of American children -- at risk.

Unwilling to face her pain over Mic & Harm, Mac is granted temporary assignment on the carrier USS Guadalcanal (along with Gunny) when the staff JAG there disappears.

Harm returns to active duty after returning from Renee's father funeral.

A Navy P-3 spy plane is rammed by a Chinese MIG and is forced to land at a Chinese Air Base. (The second such incident; the first being the actual incident that occurred early 2001)

The SecNav requests Adm. Boone re-activated to active duty, in order to travel with Harm to the Air Base to negotiate with the Chinese for the release of the plane & crew.

After the Chinese Commander is presented with photographic evidence that the MIG & its pilot that rammed the P-3 is alive & well (contrary to claims by the Chinese that the pilot was killed), the Chinese immediately release the P-3 crew; however, they would ship the P-3 back, piece by piece.

Lt. Barrett flying out to escort the plane from Chinese Air Space back to the USS Thomas Jefferson. After telling his wingman a lie to leave the escort, Lt. Barrett disobeys orders, flies into Chinese airspace & destroys the P-3 on the ground.

When a pretty female petty officer is arrested by the MP's for impersonating a Salvation Army 'bell-ringing' Santa & pocketing the cash, Harm is assigned as her attorney. However, since she has a history of unauthorized absences, she is ordered to be held in custody. But with the holidays, the brig & pre-trial detention center are unavailable, she is estranged from her father, so she must spend the holiday with Harm or with Mac.

Cmdr. Ted Lindsey (as the SecNav's administrative assistant) notifies Bud's brother Mikey that each year, the SecNav nominates 170 enlisted personnel for admission to the Naval Academy and that Mikey is being considered for one of those nomination spots. Bud & Mikey's father, a retired Master Chief though is not at all thrilled with having another son becoming an officer and insures that everyone knows it.

Harm and Mac are sent to Saudi Arabia to defend a female U.S. Naval pilot who refuses to follow the local laws and wear traditional Saudi dress and veils. Lt. Joanne Donato's outspoken refusal to be escorted by males in public and to wear proper attire causes a strain on relations between a U.S. base commander and a local Muslim cleric. It also causes Mac to feel that the lieutenant is simply being a bad soldier and disobeying orders - that is until Mac is forced to abide by the policies herself. Meanwhile, Commander Turner and Rep. Bobbi Latham have a rocky first date, making the possibility of a second seem remote until Harriet and Bud come to the rescue.

Harm prosecutes a sensitive case in an episode that sees the swearing in of a new Secretary of the Navy and the arrival of a new JAG Officer.

Shortly after assuming his new role, SecNav Sheffield appoints Lt. Cdr. Tracy Manetti, a Harvard Law grad, to Adm. Chegwidden's team. Her first assignment is second chair to Harm in a negligent-homicide case against Lt. Reynolds, a SEAL. While leading a guerrilla wargame among civilians in rural Virginia as a test of unconventional warfare, Reynolds failed to stop for local police, leading to a high-speed chase in which a deputy was killed.

A raid by agents of the Immigration & Naturalization Service (INS) on a boat carrying Vietnamese ladies being smuggled into the USA, also nets a distinguished Vietnam-native Marine Lieutenant, who is suspected to have a part in bringing the ladies in for profit.

Harm & Sturgis are assigned to see if the Lieutenants claim that he broke into the warehouse containers to steal is true, or if he really is one of the lead smugglers. They learn that when the Lieutenant was four years old living in Saigon with his mother, he was loaded onto the last helicopter evacuating people from the US Embassy in Saigon on April 29, 1975, just before the city was invaded by North Vietnam. As there was only room for 1 person left on the helicopter, his mother placed him onboard & stayed behind. He was then brought to the US & later joined the Marines, rapidly advancing through the ranks, becoming a pilot & earned great distinction for himself.

Mac is unable to accept the news that Clayton Webb really is dead and ends up in possible danger looking into Webb's "death". With the retirement of Rear Admiral A.J. Chegwidden, Cmdr. Sturgis Turner is named Acting Judge Advocate General.