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 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 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.

Bud & Lt. Singer discovers a safety file that is inadmissible in court that supports the prosecution's contention that the jumpmaster was impaired. The file mysteriously winds up in Mac's car and she thumbs through it. After conferring with Harm who tells her what she already knows, she burns the file. But during questioning court, Lt. Singer objects that Mac is basing her argument based on the file, which Bud reluctantly agrees. Mac is charged with prosecutorial misconduct, removed & replaced by Harm.

Having been chewed out by the Admiral, she takes some leave & heads to spend time with Mic in Australia, running into the Admiral & Dr. Walden who are taking their own weekend 'trip'.

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.

Adm. Chegwidden frets over a speech he must give when he is to be given an award.

Mic Brumby returns unexpectantly to the States; Mac & everyone are stunned when he announces that he has resigned his Royal Australian Navy commission so that he could move to the USA and be by the "woman he loves."

Mac comes under the glare of media scrutiny when she's named to prosecute in JAG's first televised court martial.

As Mac prepares for her televised prosecution of an innocent looking young ensign accused of murdering her husband's teenage girlfriend, she learns that her opponent is none other than Juanita Ressler, who was her professor in law school. Ressler is a very media-savvy trial attorney who uses every trick in the book to swing the media and the public over to her client's side.

Harm travels out to sea to investigate the death of a sailor aboard a carrier. Originally thought to be a suicide, Harm discovers evidence to the contrary.

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 former partner Kate Pike is considering transferring back to the JAG office. It becomes complicated when a former CO of Kate is being considered as the new Inspector General and Kate confides to Harm that he made unwanted sexual advances to her when she worked for him.

Lt. Singer appears at the door during Kate's conversation and soon afterward, the affair is reported by the Washington media, although Harm suspects Lt. Singer as the source, she denies she overheard anything.

Eventually, Kate decides that Washington is just not the place to work and decides to turn down the Admiral's job offer.

When U.S. and Turkish ships collide during a NATO exercise, Harm and Mac defend the U.S. captain, who is being made the scapegoat for political reasons.

Harm & Mac square off in court over a charge of illegal fraternization, but when they oral arguments become directed at each other & reflecting their own relationship, Judge Helfman recesses the court for the day with a strong admonishment to the both of them.

All the staff shows up at Admiral Chegwidden's house for Mic & Mac's engagement party. Lt. Singer shows up in a knock-out of a dress which stuns the Admiral for a moment, not used to seeing her in civilian clothes.

Bud shows up dress properly for once, but Harriet notices after arriving that he has peanut butter on his tie. Bud is mortified trying to get a tie from anyone, without much luck. Later, he is forced to remove his jacket when wine gets spilled all over him. Even more mortified, Bud feels desperately out-dressed.

Throughout the evening, Mac reminisces with the Admiral about past events involving the both of them.

Mac becomes upset when Harm tells her at the last minute that he will not be attending her rehearsal duty in order to complete his 6-month required carrier landing qualifications. He assures her that he will be back in time for the wedding. At the church, Chloe is still wary of being friends of Mic. On board the USS Patrick Henry, Harm learns that the LSO who will be grading him thinks of him only as a "land-based Washington weenie." His fears that he won't be graded fairly are realized when he is ordered to land after his first attempt is waved off. After convincing the LSO that they were flying they way that the LSO taught them, he allows Harm to try again. After passing, he then completes his required night traps and requests to head back to Andrews AFB. With an approaching storm, all air operations are suspended, but is assured that he & Skates can be on the first Tomcat, once its forecasted to be safe. With a break in the storm, he & Skates are allowed to go.

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.

Personal rivalries surface in the JAG office when Mac assures Harm that she'll beat him to the finish line in the Jagathon for charity. Harm then sticks his foot in his mouth by giving Mac a six-minute head start in the race. Meanwhile, testosterone levels rise when Gunny and Tiner battle head to head to see who is in the best condition for the race. And, true to form, Lt. Singer starts a betting pool on who will finish the race last, leaving Lt. Roberts feeling crushed when he discovers that his co-workers favor him.

Harm defends Lt. Barrett who readily claims he disobeyed orders and destroyed the P-3 spy plane held hostage by the Chinese because he believed it was the right thing to do. Harm and Sturgis go head to head at the lieutenant's court-martial as Harm tries to keep him out of Leavenworth, where he could be sentenced to 25 years for his actions. Meanwhile, Mac investigates a charge of sexual harassment when a female officer charges a Marine colonel with humiliating her publicly when her training tape is shown on the television show "Military Bloopers." As part of her investigation, Mac takes the Colonel up on her offer to complete her regular physical training evaluation with the Colonel. Mac recommends that the Colonel get a letter of reprimand, which could jeopardize his chance for a command.

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.

Mac's psychic vision talents come into play when a female Naval officer is found with her throat slashed in a local park. What originally seems like an open and shut case involving a love triangle that led to murder becomes much more when Mac's "visions" show her puzzling images that lead to evidence of an international conspiracy. Together with Sturgis Turner, Mac follows the clues to uncover information that leads them to a possible terrorist plot in Russia to steal nuclear weapons.

In 1944, in the midst of World War II, a disastrous explosion rocked the U.S. Navy's Port Chicago near San Francisco, killing more than 350 sailors, most of them African-Americans. Following the blast, a group of 50 sailors refused to return to work until changes were made to assure their safety. They were charged with mutiny and court martialed, but later their convictions were reversed. Now, a surviving sailor wants his record and those of all the other ""mutineers"" cleared. Asked to handle the investigation discreetly, Cmdr. Turner discovers that an injustice was done and goes head-to-head with Lt. Singer in the courtroom. Meanwhile, Harm goes house shopping with Lt. Sims.

Harm, Mac & the Admiral return to the office from the USS Seahawk after finishing up with the military tribunal. The office staff is very happy to see the Admiral back in charge, after having to deal with Lt. Singer while he was gone, with Harriet making sure the Admiral knows how ""happy"" they are.

Their joy is short-lived however, when they learn that respected Navy JAG Judge, Captain Sebring is charged with having causing an another vehicle off the road which injured the female driver & killing her 6-month old daughter. Harm is given the task of defending him, while Mac is ordered into the uncomfortable position of prosecuting him. Seeing Mac's dilemma, Cmdr. Turner offers to sit second-chair with her, so that she won't be alone.

Lt. Singer overhears Harm & Mac discussing Bud & Harriet and learns that Bud doesn't know Harriet has bought a house, while Bud hasn't told Harriet about PO Coates.

Harm and Mac investigate a "collateral damage" incident in Afghanistan when an attack on an Al Queda terrorist kills three innocent civilians. With the help of forensic pathologist Cmdr. Teresa Coulter, Mac and Harm try to find out if any of the remains can be identified as belonging to Al Queda leaders. Meanwhile, when Harm and Mac lose control of their Humvee, they are thrown into a minefield where they're forced to spend the night together figuring out how to extricate themselves from the trap.

Admiral Chegwidden, Lt. Singer & Cmdr. Turner move over to the Pentagon War Room to easily coordinate & share intelligence information on Kabir Atef's planned attack on the U.S.

When an Afghan school is destroyed in a bombing raid, Bud & PO2 Coates fly to the scene to survey the damage. Once there, he promises to the locals that the US will re-build the school.

Meanwhile, Harm & Mac are still in Afghanistan attempting to pick up Kabir's trail, still looking for the mysterious truck that disappeared during a raid. ("In Country"). They come under fire, but are unhurt. Once they repair the damage to the vehicle caused by the gunfire, they continue driving all night and find an abandoned truck that appears to be the one they're looking for. They find the driver dead of suspected origin. Continuing onto the next village, they find villagers in the same condition. A medical team is brought in and they determine that the villagers are suffering from radiation poisoning.

The episode starts with a short recap of where we left off last season: Bud & PO Coates walking along a dirt road enroute to attend the ground-breaking of the new school, when they spot a small boy playing in a field that had yet to be cleared of mines. As Coates runs for help, there is an explosion behind her. She turns in time to see Bud injured in the explosion and runs to his side. Coates insists that Bud must be transported on the helo that brought them in, that Bud won't be able to wait for the proper medevac chopper.

Bud is airlifted to a field hospital, critical, but still alive. As luck would have it, ZNN reporter Stuart Dunston just happens to be at the base camp when Bud is brought it. Dunston reports the arrival of an injured JAG officer that was brought it, but does not report the name. Chegwiggen advises Harriet, but reminds her he is still on the Seahawk. She tries to contact him by instant messaging, but does not receive a reply.

The future of seven seamen hang in the balance due to Lt. Singer's recommendation of court martial for all of them following a mishap on the ship. However, Singer's career could also be doomed if the father of her unborn child is someone on the Seahawk, and it's Harm and Mac's job to find out who it is. The problem is, the career-oriented Singer isn't talking, so Harm enlists the help of Lt. Manetti to do some sneaky behind-the-scenes investigating in order discover the identity of the father.

Harm and Lt. Cmdr. Manetti travel to Naples, Italy when an Interpol officer believes someone aboard a US destroyer is a serial killer who has killed four women while on leave in European ports.

Mac remains onboard the USS Seahawk until a replacement for Lt. Singer is assigned. (See ""Notes"" below)

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.

Mac is called in to minimize the damage after a Navy lieutenant blows the whistle regarding deficiencies in a top-secret Navy combat device. When she helps the lieutenant get released from the military, she is furious when she later discovers that he had stolen hi-tech secrets to use in his video-game company.

Meanwhile, Harm is threatened with a lawsuit by an elderly lady and her shady lawyer following a minor traffic accident.

NCIS Agent Gibbs continues his investigation on the terrorist, Amad Bin Atwa to avert another attack on a Navy ship. Harm is court-martialed for the murder of Lt. Singer.