Fresh out of law school and fresh into the Navy, Lieutenant Daniel Kaffee (TOM CRUISE) has coasted along on negotiating plea bargains, 44 so far that have not required extensive time in a courtroom. It's for that reason that he's assigned a case that would seem to have the same outcome, that of two Marines -- Lance Corporal Harold W. Dawson (WOLFGANG BODISON) and Private Louden Downey (JAMES MARSHALL) -- stationed at Guantanamo Bay, Cuba, who roughly woke up a fellow Marine, stuffed a rag into his mouth and taped over it, and tied his hands and feet with the same tape. A plea bargain in this case, and no further trouble. That seems to be the consensus.
It's the brick wall Lieutenant Commander JoAnne Galloway (DEMI MOORE) faces when she asks Captain West of JAG Corps to assign her as lead counsel for the defense on the case. West believes her not to be experienced enough to take this on. Enter Kaffee and enter initial conflict, as the two sides assess each other and don't like what they find. Galloway doesn't like how Kaffee coasts along, not making enough of an effort in his casework. Kaffee doesn't like Galloway stepping in front of him to attend to certain matters, when he is the one in charge of the case, despite Galloway being his superior officer in this case.
But there is bigger conflict for the two of them, and Kaffee's assistant and friend Lieutenant Sam Weinberg (KEVIN POLLAK), when a visit to Guantanamo Bay introduces them to Colonel Nathan Jessep (JACK NICHOLSON), head of operations on the base. He claims everything a lesser attorney might want to hear in order for the case to be closed quickly: Nothing out of the ordinary happened and move along, please.
But the murdered Marine had asked repeatedly in letters to various persons of rank to be transferred off the base, knowing that he couldn't handle what was required in training exercises, yet Jessep ignored those pleas. A transfer? No. Not when Washington beckons with a possible high-ranking position in the National Security Council. Something's amiss here, these two men could not have acted on their own, and that becomes the centerpiece of the case.
Kaffee also struggles with his own identity, as his late father was the attorney general of the United States at the time of the civil rights movement, and apparently a major trial lawyer in his own right. So what should he do? Be a bigger man, or be as he has always been, ratcheting up another plea bargain for his clients and moving on silently rather than contend with the prickly Colonel Nathan R. Jessep (JACK NICHOLSON), the head of the Marine base at Guantanamo.