Harm is assigned to escort a rambunctious and ravishing Romanian princess, whose life has been threatened if her father petitions to join NATO. Meanwhile, Bud wrestles with starting a romance with Ens. Harriet Sims.

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.

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 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.

Adm. Boone (CAG aboard the USS Seahawk, ""A New Life"" & ""Chains of Command"")is nominated to become the Sixth Fleet Commander. An anonymous informant accuses Adm. Boone of massacrering civilians during the Vietnam War, and Harm and Mac are given only four days to investigate the claim, in part one of a two-part episode.

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's chance of being rescued from the Atlantic Ocean hinges on Mac's psychic ability (first seen in Season Five's "Psychic Warrior"). However, Mac is trying to cope with her conflicting emotions for both Harm & Mic. On the edge of going unconscious from severe hypothermia, Harm's fires several warning shots which attracts the rescue helicopter. Back onboard the USS Patrick Henry, Harm's vital signs start to fade out, but Skates words help him pull through. Transferred to Bethesda Hospital, Renee learns that Harm has partial amnesia and doesn't remember them being a couple over the past year. Mac's indecision about the wedding drives Brumby back to Australia. When Harm tells Mac on the phone to come to his place so that she doesn't have to be alone, she arrives only to learn that Renee has beaten her to Harm's place with the news that her father has died. Mac ends up in the rain with no one around.

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.

""AUGUST 7, 2001""

Following the transfer of a U.S. Marine accused of rape from the local Indonesian police to his CO at the Indonesian consulate, the consulate comes under siege by angry, armed locals.

When the commander of the Marine detachment is killed and his next-in-command is blinded during the surprise attack, Mac realizes that she is next in command and must organize the emergency evacuation of the consulate under fire.

Back at JAG, Harm defends a SEAL accused of killing a person onboard a flight that Harriet was a passenger.

**October 20, 2001**

While filling in at Patuxent River for pilots that have been deployed overseas, Harm learns his friend, Cmdr. Scott Webster is being charged with fraternization with his RIO. Harm is granted permission to search his clients computer for any communication with his RIO which could be used against him. Cmdr. Webster receives a call that his son has been arrested for speeding & freeing to elude. Cmdr. Webster leaves Harm alone at the house while he picks up his son. Going through the hard drive, Harm discovers information that he might be considering selling national secrets, but attorney-client privilege prevents Harm from disclosing that information and his client does not wish to discuss it.