Mac's ""little sister"" unexpectantly shows up at JAG headquarters, declaring that she's run away from her abusive stepfather. While she investigates whether Chloe has been abused, Mac has her hands full keeping her from turning the office upside down, then learns that her real father is still alive serving on a ship in the Navy. Despite the cost, Mac convinces the Admiral to allow the two to talk to each other via satellite video-conferencing.

Meanwhile, Harm spends the evening interrogating a beautiful Navy doctor arrested for DWI after she lost control of her vehicle on icy roads and ran over a Nativity scene. Harm agrees to defend her when he learns that just before the accident and before she took the breathalyzer test, she had drank some liquid cold medicine (which contains 25% alcohol)

Adm. Chegwidden's attempts to fly to Italy to spend Christmas with his daughter, however, with the Washington, DC area mired in snow, most of the flights out have been cancelled.

When Harm and Mac set out to find C.I.A. Agent Clayton Webb's killer after his body is found aboard a burning ship, they inadvertently uncover a rogue government spy agency.

Retracing Webb's steps, Harm and Mac learn that he was on a top-secret mission to deliver a high-tech weapons project to the proper authorities when he was stopped. Waiting for Harm and Mac when they discover this, though, is none other than Harm's former nemesis, ex-C.I.A. Agent Clark Palmer, now working with the rogue spy agency, who will stop at nothing -- including Harm's murder -- to get his hands on the top-secret project.

Bud's first case as a newly sworn in JAG attorney is to defend his father, a retired Navy Chief who's been accused of having been involved in defrauding the Navy when he was in charge of Ship's Stores. Though the two have been estranged, Bud feels a strong obligation to his father, who specifically requested him to be his attorney. Harm is the designated prosecutor, which spooks Bud, as he knows he's going up against the best.

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.

As Harm considers his future at JAG, he learns that Charlie Lynch -- the ex-Navyman responsible for the murder of Annie, the abused child whose death still haunts Harm -- has resurfaced, placing the little girl's twin sister, Dar-lin, in danger. Putting his career decision on hold until he closes the chapter on Lynch, Harm tracks him to a shipyard where the vicious killer is holding Dar-lin hostage. Overflowing with anger against all Lynch's grisly acts of murder, Harm finds himself in an intense stand-off with him that will leave only one man standing.

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 is stunned to learn that his former girlfriend, Lt. Cmdr. Jordan Parker has been found dead in her apartment, having been shot with her own gun.

Despite this evidence, Harm is unwilling to accept the premise that Jordan committed suicide & calls in Lt. Cmdr. Teresa Coulter to help examine the forensic evidence. Harm & Mac begin to look for possible suspects who would want to kill her, starting with her last boyfriend who had also been a patient of hers.

However, as each of the suspects are ruled out, they begin to look for other possibilities to explain her death. The investigation leads to a shocking discovery for Jordan's neighbor. Returning home, Harm is stunned to find a letter from Jordan in his mail. Jordan wrote & mailed it a few hours before she was killed; in which she tells Harm just how much she had valued their time together.