Members of the "JAG" staff are "helped" along to discover their true inner feelings while celebrating Jennifer Coates promotion to Petty Officer 1st Class.

Preparing to give a lecture about an 1842 Naval court-martial, Mac finds herself daydreaming about what actually happened.

Harm defends a Sergeant Major accused of the attempted murder of his wife. However, the Sgt. Major claims that he was concerned when his wife didn't come home, went out looking for her & was led to her location by the vision of a deceased chaplain from his old Vietnam unit. His defense attracts a representative of the Vatican which is considering the deceased chaplain for Sainthood. Meanwhile, when Tiner hooks up a new screensaver that searches for extra-terrestial life on the Admiral's computer, it stirs excitement when it starts making weird noises.

Harm represents the divorced Marine colonel Anderson who has overextended his custody agreement when attempting to spend time with his son before his mother moves him far away. But a warrant goes out to for Anderson, on whom the Vietnam war left its marks. After a local deputy attempts to arrest him without success, a strong police force goes after him. Harm learns what Anderson is really up to and helps him to reach a lodge, the place where he promised to bury an old pal who died back in Vietnam, but was left behind. Locations: Vietnam (1972); California (Tustin, Santa Ana,Big Pine, Bishop)

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.

When civilians are killed in a bombing raid, an International Criminal Court charges the United States with war crimes and the SecNav is the one on trial representing the USA. The SecNav is defended by Harm, Mac & Bud who find they must also defend the United States decision for waging the war. At the end, the court finds the USA on the following charges: Crimes against humanity - Not Guilty War Crimes - Not Guilty Intentionally targeting non-combatants - Not Guilty Willful destruction of civilian property - Guilty. The court orders the USA to provide reparations to the town of Tikifa in the amount of $20 million US dollars. The prosecutor mentions to the SecNav that he doesn't agree with the verdicts, but pleased the SecNav won't have to go to prison. In response, the SecNav states that the two countries have been friends for too long and they both go off to get a drink together.

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.

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.

Mac is assigned to represent an Arab princess not only at an INS hearing but also before an Islamic court, when the woman elopes with a Naval Petty Officer who is accused of smuggling her into the United States. When AJ talks to Dr. Walden about what happened to his car, she is appalled that AJ would accuse her son of impropriety & terminates their relationship. Danny Walden is quite smug to AJ that he had been able to break them up -- which will come to haunt him later. With his car still being held by the police, he is dismayed with driving a rental car. Harriet goes into labor 4 weeks early and a seemingly positive childbirth turns sour when it is discovered that the baby's head is pressing against the umbilical cord cutting off blood supply to the baby and her doctor (Dr. Gettis) is nowhere to be found. As another doctor steps in, Harriet is wheeled to the operating room in an attempt to save the baby.

A Marine captain has deserted and has become a freelance warlord in Afghanistan, seeking Osama bin Laden; the Afghan government places him on trial; Harm and Mac defend him; Islamic justice follows. The Navy recalls Bud Sr. to active duty.

Harm and Meg are investigating the death of a Navy officer at the Arlington Cemetery, where during the months before, other Navy officers have been murdered, too. This murder happened after a reception at the French embassy and the trail leads to the Thai ambassador and his wife. Harm is attracted to her as she reminds him of a girlfriend back in Vietnam who was killed. Also, Colonel Patano (the ambassador's guard), is one of the suspects. Locations: Washington D.C.; McLean, Va.; Bethesda, Md.

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 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.

Due to overloaded JAG caseload which was made worse by the review of all of Cmdr. Imes cases, the Admiral has the SecNav re-instate Harm's Naval Commission, clearing the way for Harm to return to JAG. When a US submarine rescues 10 North Koreans after their vessel sinks in South Korean waters, Cmdr. Turner arrives from Washington to determine their purpose.

Guards at Guantanamo Bay are ordered to remove a detainee from his cell for interrogation. He resists, so the guards try to subdue him and end up putting him in a coma. It turns out the "detainee" was a disguised soldier and the whole thing was a training excercise. Harm is assigned to defend the guards while Mac argues that torture and excessive force are not appropriate even when dealing with terror suspects. Back in Washington, Bud and Mikey Roberts go shopping for shoes and get into a disagreement with another customer that escalates into violence.

Harm & Mac are sent to Belfast, Ireland when the child of Navy Lieutenant Nivens suddenly turns up missing and a note left behind indicates it was taken by Lorcan Barnes of the Irish Republican Army (IRA), who also happens to be the child's father. Arriving in Belfast, Harm & Mac are immediately at odds with the Royal Police, when they suggest ""negotiating"" with the IRA for return of the baby. Not finding much help, they go and search out the IRA on their own. Directed to a bar & told to ask for a particular type of beer. While playing darts, a man showing Mac the proper way to throw a dart whispers in her ear to go to an abandoned storefront. With the Royal Police tailing them, Harm and the baby's mother risk going to the storefront, while Mac boards a bus and leads the Police away from Harm.

Due to frustration at being unable to wrest custody of his son from his drug addicted wife, Corporal Wetzel was distracted during a war game exercise and crashed a tank. Accused of dereliction of duty, Wetzel admits to being diverted on the job, but insists that Mac and Harm must keep him out of jail, since his arrest would certainly mean losing his son. Harm and Mac like Wetzel and understand that his frustration accounts for his poor judgment. But nobody's more surprised than they when Wetzel winds up in a tank in a stand-off with the military, questioning why he's being forced to choose between being a marine and being a father.

Political pressures come into play after an F-14 pilot clips a ski helicopter during a NATO exercise over Italian airspace, killing six civilians. Harm and Mac are assigned to opposite sides in the case, but the Italian government wants to prosecute on its own.

When the captain of a U.S. Navy frigate rescues a young girl in Cuban waters and sets off the beginnings of an international incident, Harm and Bud's investigation leads them to Cuba and a meeting with Castro.

Harm defends a female pilot accused of sexual harassment by a member of her crew who claims she ruined his future in the military because he rebuffed her advances. Harm is skeptical of his client's denials of the charges, while his co-counsel, Lt. Cmdr. Manetti, is sympathetic, causing tension between the JAG lawyers. Prosecutors Mac and Sturgis seem to have an open and shut case with their star witness testifying until Harm throws them a curveball that throws the case wide open.

While conducting a flight test, Harm ends up involved in a serious CIA mission, over North Korea. In Iraq, a Marine recon platoon is surprised by a 10 year-old Iraqi unarmed civilian tending to his goats. Surprised at seeing the armed Marine, the boy runs off. Later the platoon is involved in a skirmish, resulting in two deaths and the Sergeant losing their radio. Unable to call in for transportation out of the desert, the platoon must end up walking many miles in the desert to safety. Once safe, it is learned that the firefight was the result of the boy returning to his village & notifying some of the local Iraqi resistance members, who immediately went out to engage the platoon.

Navy SEAL's come under the microscope when a large amount of heroin is intercepted and confiscated, only to have a kilo of it turn up missing. And Bud comes to the aid of a Marine singer who is being harassed by the record company that he is under contract to, when they object to him serving in the war.

The car belonging to a Navy Commander assigned to a Bio-Weapons Defense Laboratory is found abandoned on a bridge across the Potomac River. Harm & Mac work with FBI agents in the investigation.

It's Christmas Eve. Col. MacKenzie crashes her car on the way home, and while unconscious through a series of episode flashbacks and discussions with a base therapist deals with many of her issues including infertility, insomnia, loneliness, Webb, and Harm.

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.