The narrative of the film begins with the presenting of two families, The Stonemans--a Northern abolitionist family, and The Camerons--a Southern family. This is during the time just before the Civil War, and Ben Cameron sees a picture of Elsie Stoneman and falls in love with her beauty even though he hasn't met her. Once the War begins each family's sons enlist for their respective armies. This separates the Stoneman sons from marrying the Cameron daughters for the time being. Two of the Cameron brothers are killed along with the younger Stoneman brother. Ben survives, but is captured by the North and taken to Washington D.C. where he is treated at a hospital for his wounds but he soon learns he will be hanged. While at the hospital he meets Elsie who helps Ben's mother to come to his aide.
Mrs. Cameron goes to see President Lincoln in order to plead for a pardon from him. Lincoln is assassinated soon after by John Wilkes Booth during a play at Ford's Theatre. The film moves into the Reconstruction era post-Cival War. We see many black voters who have come out to vote in favor of black representatives in legislature. While this is happening, Ben who has his pardon forms the Ku Klux Klan in order to fight back against blacks having rights in the South. Because of this Elsie no longer will be with Ben as her loyalty is to her father and to the ideals which he has set for their family to be in line with abolition. Soon after Flora Cameron is approached by a black man, Gus who's been freed through the war being won by the North. Flora is scared of the man and kills herself by jumping off a cliff rather than be approached any closer by Gus. This stirs Ben's hatred and causes him and his Klansmen to hunt down and lynch Gus as they blame him for Flora's death.
Meanwhile Lynch, who is Stoneman's protege, seeks to stop the Klan from murdering more black people out of their hatred. Lynch also is able to win a legislation that allows mixed-race marriages. This further divides the characters of the film as Ben continues on as leader of the Klan, and when he finds out that Lynch wants to marry Elise he comes to her aide to ensure Lynch doesn't marry her. Ben's Klansmen capture Lynch and take control of their town once more and when the next round of voting for legislation happens we see members of the Klan surrounding the polling place to intimidate the black people from voting with threats of violence and death if they do. The movie ends with two weddings between the Stoneman and Cameron families. Ben marries Elsie and Phil Stoneman marries Margaret Cameron, and we see a giant figure that wields a sword upon a horse appearing to oppress the people followed by the image of Jesus superimposed over everyone as they rejoice. The final words on-screen of the film are, "Liberty and union, one and inseparable, now and forever!"
