As the Civil War sweeps across the country, it finds the most wayfaring member of the Brannon family of Culpeper County, Virginia, working as a wharf rat at the Mississippi River port of New Madrid, Missouri. Caught up in a bar fight he tried to avoid, Cory Brannon is rescued by Captain Zeke Farrell, of the riverboat Missouri Zephyr, who offers him a job as part of his crew.

The Zephyr makes the journey from New Madrid to New Orleans in late 1861. A year later, the Zephyr reaches Cairo, Illinois, and is greeted by Union gunboats. The war is now on the water, and there is little room for river commerce.

When Cory learns that a Union force under Ulysses S. Grant is advancing toward the forts to claim the area for the North, Cory and his crewmates must choose sides and join in the fight to see which side will control the river.