A hotshot young Navy lawyer, Lieutenant Daniel Kaffee, is assigned to defend two Marines, Private First Class Louden Downey and Lance Corporal Harold Dawson, who are accused of the murder of a fellow Marine at the Guantanamo Bay Naval Base in Cuba. Known for seeking plea bargains instead of taking cases to court, Kaffee initially treats the case with his usual casual demeanor. The defendants claim they were acting under orders in the form of a "Code Red," an unofficial disciplinary measure not sanctioned by military law. Kaffee's skepticism about the merits of their case wanes as he digs deeper, even clashing with his co-counsel, Lieutenant Commander JoAnne Galloway, who insists that the case should go to trial to uncover the truth.

The investigation reveals a possible cover-up led by the base commander, Colonel Nathan R. Jessep, who may have ordered the Code Red on the deceased Marine as an act of retribution. Under the stern eye of the judge, Kaffee begins to step up, abandoning his penchant for plea bargains to take on an entrenched military establishment. As he and his legal team prepare for a high-stakes court-martial, they confront issues of honor, duty, and the moral complexities embedded within the Marine Corps. The trial becomes not just about the fate of the two accused Marines, but also about the integrity of military values and the nature of truth itself.