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.

Mac is assigned the personally distasteful task of representing a fellow Marine who is appealing his death sentence for the murder of three other Marines. She believes that the defendant, Kenneth Farmer, should receive the death penalty, but she must argue otherwise in court. Brumby, who doesn't believe in capital punishment, must argue in favor of it.

However, in attempting to overturn the original guilty verdict, Mac must argue inadequate counsel by the corporal's previous lawyer: then-Commander A.J. Chegwiggen. The appeals court lets stand the original guilty verdict, but orders a new sentencing hearing.

Mic is recalled by the Royal Australian Navy and must leave within 72 hours. As a result, Harm is assigned to replace Brumby at the new sentencing hearing. Despite Mac's arguments to the defense of Corporal Farmer that was not raised by then-Commander Chegwiggen, Corporal Farmer is again sentenced to death.

Admiral Chegwiggen throws a goodbye party for Mic at the local bar.

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.

Harm defends a Sergeant Major accused of the attempted murder of his wife. However, the Sgt. Major claims that he was concerned when his wife didn't come home, went out looking for her & was led to her location by the vision of a deceased chaplain from his old Vietnam unit. His defense attracts a representative of the Vatican which is considering the deceased chaplain for Sainthood.

Meanwhile, when Tiner hooks up a new screensaver that searches for extra-terrestial life on the Admiral's computer, it stirs excitement when it starts making weird noises.