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 Capt. Zeke Farrell of the riverboat Missouri Zephyr. Later, when a small party of men attempts to burn the boat, Cory sounds a timely warning and finds himself the newest member of the crew. The Zephyr makes the journey from New Madrid to New Orleans in late 1861. During this time, Cory matures and finds that he has an interest in the ways of the rivermen and in the captain's daughter, Lucille. Later, in early 1862, 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 Farrell, his ship, and his cargo head down the Tennessee River to avoid Union harrassment, they are drawn into the battle lines around two strongpoints on the river: Confederate Forts Henry and Donelson. A Union force under Ulysses S. Grant is advancing toward the forts to claim the area for the North, and Cory and his crewmates join in the fight to see which side will control the river. Captain Farrell is killed when the Zephyr is destroyed by a Union gunboat.
Taken prisoner, Cory loses contact with Lucille. When he learns that Grant is preparing to move farther south, he tries to alert Southern leaders of the danger growing in Western Tennessee. Again he takes up arms, this time at the battle of Shiloh, where the armies in the West collide to determine the fate of the war in the western theater.