John Carlile is a young man growing up in tumultuous antebellum Baltimore, Maryland. He comes from a well-off merchant family, but their wealth originates from smuggling and bootlegging. He is sent to military school for the discipline and education, but the death of his mother then his younger brother along with the loss of a romantic interest cause him to run off to sea, against his father's wishes.

What follows are the stories of his adventures until he decides to resume his education, attending medical school. His impulsive instincts cause him problems, but he finally puts his life together and he starts a medical practice in Richmond, Virginia. This situation is enhanced when by chance he encounters his old love who is now a widow. They marry and everything is blissful until she dies in childbirth, leaving him with a baby daughter.

He goes off the deep end, neglecting his affairs before finally getting himself together by returning to the sea and practicing as a ship board physician.

When the Civil War erupts he decides his sympathies lie with the south, and he offers his services to the Confederacy as a naval surgeon. It turns out they have no use for him in that capacity. Instead using his organizational talents first to set up and supply naval infirmaries then they send him to Liverpool, England to assist in outfitting commerce raiding ships.

He sails aboard the CSS Alabama in an uncertain role. Returning to England, he resumes his role outfitting a new commerce raider but his impulsiveness results in offending a woman of means there. He is transferred as a result to Montreal, Canada, assigned to the Confederate Secret Service.

This story follows his escapades using sailor yarns to outwit his enemies, engaged in activities designed to change the outcome of the American Civil War.