Part 1: Civil War of United States

Phil, the elder son of the Stonemans (a Northern family), falls in love with Margaret Cameron (the daughter of a Southern family), during a visit to the Cameron estate in South Carolina. There, Margaret's brother, Ben, idolizes a picture of Elsie Stoneman, Phil's sister. When the Civil War arrives, the young men of both families enlist in their respective armies. The younger Stoneman and two of the Cameron brothers are killed in combat. Meanwhile, a black militia attacks the Cameron home and is routed by Confederate soldiers, who save the Cameron women. Leading the final charge at the Siege of Petersburg, Ben Cameron earns the nickname of "the Little Colonel", but is also wounded and captured. He is then taken to a Union military hospital in Washington, D.C.

During his stay at the hospital, he is told that he will be hanged. Working there as a nurse is Elsie Stoneman, whose picture he has been carrying. Elsie takes Cameron's mother, who had traveled there to tend her son, to see Abraham Lincoln. Mrs. Cameron persuades him to pardon Ben. When Lincoln is assassinated, his conciliatory postwar policy expires with him. In the wake of Lincoln's death, Elsie's father and other Radical Republicans are determined to punish the South.[21]

Part 2: Reconstruction

Stoneman and his protégé Silas Lynch, a psychopathic mulatto head to South Carolina to observe the implementation of Reconstruction policies. During the election, in which Lynch is elected lieutenant governor, black people stuff the ballot boxes, while many white people are denied the vote. The newly elected members of the South Carolina legislature are mostly black.

Inspired by observing white children pretending to be ghosts to scare black children, Ben fights back by forming the Ku Klux Klan. As a result, Elsie breaks up with him. While going off alone into the woods to fetch water, Flora Cameron is followed by Gus, a freedman and soldier who is now a captain. He tells Flora he desires to marry her. Uninterested, she rejects him, but Gus keeps insisting. Frightened, she flees into the forest, pursued by Gus. Trapped on a precipice, Flora warns Gus she will jump if he comes any closer. When he does, she leaps to her death. While looking for Flora, Ben sees her jump and holds her as she dies. He then carries her body to the Cameron home. In response, the Klan hunts down Gus, tries him, finds him guilty, and lynches him.

After discovering Gus' murder, Lynch orders a crackdown on the Klan. He also secures the passing of legislation allowing mixed-race marriages. Dr. Cameron is arrested for possessing Ben's Klan regalia, now considered a capital crime. He is rescued by Phil Stoneman and a few of his black servants. Together with Margaret Cameron, they flee. When their wagon breaks down, they make their way through the woods to a small hut that is home to two former Union soldiers who agree to hide them.

Congressman Stoneman, Elsie's father, leaves to avoid being connected with Lynch's crackdown. Elsie, learning of Dr. Cameron's arrest, goes to Lynch to plead for his release. Lynch, who lusts after Elsie, tries to force her to marry him, which causes her to faint. Stoneman returns, causing Elsie to be placed in another room. At first Stoneman is happy when Lynch tells him he wants to marry a white woman, but he is then angered when Lynch says that it is Elsie he wishes to marry. Elsie breaks a window and cries out for help, getting the attention of undercover Klansman spies. The Klan gathered together, with Ben leading them, ride in to gain control of the town. When news about Elsie reaches Ben, he and others go to her rescue. Lynch is captured while his militia attacks the hut where the Camerons are hiding. However, the Klansmen, with Ben at their head, save them. The next election day, blacks find a line of mounted and armed Klansmen just outside their homes and are intimidated into not voting.

Margaret Cameron marries Phil Stoneman and Elsie Stoneman marries Ben Cameron.