Blackwater Betrayal tells the story of the ruthless, ill-conceived scorched earth actions by the Confederacy of Mill Town, or Milton, on the Blackwater River in the Western Florida Panhandle and the rest of the Pensacola Bay area. It tells the journey of John Geoghegan and how he became a successful blockade runner out of Pensacola. It is the story of Maria Moreno, the Spanish beauty whom John loves and almost loses. It is the story of John's friend Ben Jernigan, engaged to French-educated Amanda Rucker. Ben has no interest in war, so he hides in Yellow River swamp to avoid conscription but finds himself drawn out to help his friend Caleb, a slave who has killed in self-defense. He gets Amanda and her friends out of Milton and finally leaves the Southern ruins with John and his friends on his ship, the Carolina.