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.

With Harm's eyesight fixed, Harm decides to go ahead and submit a request to be transferred to a fighter squadron. When Lt.Cmdr Parker finds his written request, she is upset at the prospect of Harm being gone for months at a time.

Afterwards, Harm goes over to Mac's apartment who has Chloe spending the night with Mac before she is reunited with her real father. Harm informs Mac of the eye surgery and his plans. Mac is equally upset at the prospect of losing Harm. Mic shows up at Mac's apartment after Harm leaves attempting to court Mac's feelings. After Mic leaves, Chloe tells Mac that Brumby and Harm have a crush on her and begins teasing Mac: ""Harm & Mac, sitting in a tree, k-i-s-s-i-n-g.""

Admiral Chegwidden passes Harm's request to be transferred onto the SecNav. Not willing to do any favors for Harm, the SecNav is reluctant to intervene.

Unexpectedly, the wily Buxton demands that Harm and Brumby be his lawyers, thereby preventing Harm from testifying against him and forcing the two adversarial lawyers to work together. The contentious trial continues with Mac and Roberts prosecuting, and the pressure is enormous as the U.S. Navy and the Russian government vigilantly follow the trial to ensure that its own agendas are met. Meanwhile, the Navy has its own special plans for the troublesome Buxton.

Admiral Chegwidden welcomes Harm back to JAG by assigning him a tricky case - defending the son of the Secretary of Navy. Harm takes the case when Lt. Nelson, the son of the Secretary of the Navy, is accused by Cmdr. Burke of disobeying an order at sea, an act worthy of a court martial.

Harm and Mac are sent to Panama to investigate the wife of a Marine officer, Olivia Dunston, suspected of smuggling drugs into the U.S. When faced with the evidence, Olivia feebly denies the allegations, leaving Mac thinking that she's guilty of the charges.

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.

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."

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.

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.

Mac becomes ""Acting JAG"" as Admiral Chegwidden is selected to head the Promotions Board for Captain.

Harm takes up the defense of a former Marine Drill Instructor who is facing life imprisonment under the 3 strikes law.

Cmdr. Ted Lindsey (last seen in ""People vs. Mac"") tries to impress the Admiral & Mac in an attempt to earn promotion to Captain.

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.