The narrative opens in Washington and the Carolinas in the immediate aftermath of the Civil War, capturing the national chaos following Abraham Lincoln's assassination. The plot unfolds around the political machinations of the Radical Republican leader Austin Stoneman and the fierce resistance of the Southern gentry. A central storyline follows the romance between Stoneman's daughter Elsie and the Confederate veteran Ben Cameron, highlighting the personal divisions caused by sectional animosities.
As the story develops, the focus shifts to the southern reconstruction, where freed slaves are politically enfranchised and organized through secret societies like the Union League, leading to a reign of terror and political corruption. The traditional southern aristocracy faces economic ruin through heavy taxation and land confiscation policies championed by Northern politicians. In response, Ben Cameron organizes the Ku Klux Klan as an invisible empire to challenge the new regime and restore white supremacy through clandestine violence and midnight raids.
The narrative vividly portrays the political battles in Washington, including the failed impeachment of President Andrew Johnson, which leaves the radical faction free to impose harsh military rule over the conquered states. The social fabric of the South disintegrates under the pressure of carpetbagger rule and the radical transformation of racial hierarchies. Personal conflicts culminate in dramatic confrontations, courtroom trials, and acts of violent retribution across the Carolina foothills.
The novel reaches its climax as the clandestine organization asserts its power, successfully overturning the Reconstruction government in the region through coordinated force. The ending hints at a permanent realignment of American society, where the old order is forever destroyed, leaving the South scarred by racial conflict but poised to rebuild its society under a new and bitter reality.