Harm and Meg investigate the theft of stolen missiles at the SEATAC Naval Base. While interrogating PO1 Quinn of the theft, a prison-break takes place and Lt. Austin is taken hostage. Contrary to the Major in charge, Lt. Rabb thinks that this is a well-planned breakout with a big goal. Locations: SEATAC Island Naval Base and surrounding areas

Harm is called in to probe the death of Navy pilot Lt. Marion, son of US Senator Grace Marion, while training with the Navy SEALS. As he was there only for two days, it seems that the death was due to gross negligence. With the reports given by his superior and comrades, combined with the results of how how he died, it seems that the actual incident is a cover-up. Analyzing his equipment and learning that it was a combat mission (and not a training mission as stated), the facts then point at murder. The key to all this could be General Behnke. Locations: Washington D.C.; NAS Roosevelt Roads, Puerto Rico; Carribean Sea; Colombia

Millions of viewers are turned into witnesses when they see a Marine guard shoot an arrested terrorist on live television, and its Harms job to defend him. With Mac on the prosecution, she and Harm are pitted against each other in what seems like an open and shut case of cold-blooded murder. But when Harm is replaced by a civilian attorney with a defense plan that doesnt add up and whose fees are being paid by a wealthy right wing industrialist, Percival Bertram. Harm decides to do some investigating of his own.

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 is trapped below deck on a sinking ship with a sailer, who has been accused of murder, and a guard. Some rescue equipment collapses, blocking the only escape route. As water begins to fill the room, the three men are certain that the situation is hopeless.

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 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.