Cory Brannon's fortunes change when he helps Zeke Farrell defend his riverboat, the Missouri Zephyr, from a mob of Unionists out to burn it. For months, Missouri has been torn between the Union and the Confederacy, with frequent skirmishes in which both sides claim victory. Aware that Federal forces are moving into Illinois, from which they could control the Mississippi, Zeke and Cory decide to make a dash for Confederate waters, taking with them Zeke's daughter, Lucille, who has captured Cory's heart. Landing at Fort Henry, the two men are recruited by the Confederates to defend the fort while the main body of troops and civilians escape. Zeke sends Lucille to Mississippi to live with relatives. Zeke is killed during the battle and Cory heads to Nashville to let Lucille know of her father's death. There he learns that Union troops are headed west to Pittsburg Landing on the Tennessee, where Grant is preparing an attack on Corinth, Mississippi. Southern troops in the West are headquartered there.
Slipping out of Nashville, Cory heads for Corinth to warn the Confederates, who are already aware of Grant's intentions and are preparing to attack his position before the Yankee general's entire army can arrive. Cory is caught up in the ensuing battle - long, hellish, and by far the bloodiest fighting so far in the war - near an old, little-used Methodist meetinghouse known as Shiloh Church. He survives the battle unscathed, but he has seen things that will change him forever.