Adm. Chegwidden agrees to help the White House with an event honoring Medal of Honor recipients, but only if he can investigate the case of a vet who was dropped from the list because of a shoplifting arrest. Meanwhile, Mac and Harm look into a fire aboard a destroyer.

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.

Harm doesn't have much hope in his defense of a two-star general court-martialed for disobedience and reckless endangerment during a wargame. His job is made more complicated when, in a rare move, Mac is appointed as the judge.

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.

Cdr. Turner gets to hitch a ride on a submarine that is bound for the mideast when it has been discovered that a 10-kiloton nuclear warhead has turned up missing.

Having felt betrayed in the past by the present members of JAG, Commander Lindsey delivers his report to the SecNav critical of the Admiral & the rest of the staff at JAG.

A year ago, Sturgis was assigned to prosecute Bud against charges that Bud was derelict in his duties while representing his client in court. Now, Sturgis competency in handling a case is questioned and Sturgis must now rely on Bud to successfully defend him.

When the CIA learns that a drug lord is attempting to sell missiles to terrorists, Clayton Webb (re-assigned to South America in "Need to Know") is assigned to prevent the deal from going through. To help with his cover, Mac is sent from Washington to masquerade as Webb's pregnant wife.

In Paraguay, Mac & Webb continue their mission to thwart the drug lords & terrorists.

Harm continues to deal with his emotions where Mac is concerned. Worried about her, Harm turns to CIA Attorney Catherine Gale for help in determining Mac's location. However, Harm ends up helping Ms. Gale with a personal issue.

As Harm now has custody of Mattie, PO2 Jennifer Coates agrees to move into an apartment down the hall from Harm. Admiral Chegwidden looks into why the diamond he gave to Meredith for their engagement ""just doesn't look right"".

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

Mac learns to be careful what she asks for - as she is assigned to escort a female Marine prisoner, after having made the request that the prisoner should be escorted by someone able to control her.