The film follows two juxtaposed families: the Northern Stonemans—abolitionist Congressman Austin Stoneman, based on the Reconstruction-era Congressman Thaddeus Stevens,[14][15] his two sons and his daughter Elsie—and the Southern Camerons, a family including two daughters, Margaret and Flora, and three sons, most notably Ben.
The Stoneman brothers visit the Camerons at their South Carolina estate, representing the Old South. Phil, the elder Stoneman son, falls in love with Margaret Cameron, while young Ben Cameron idolizes a picture of Elsie Stoneman. When the Civil War begins, these young men enlist in their respective armies.
A black militia acting under a white leader ransacks the Cameron house; the Cameron women are rescued by Confederate soldiers who rout the militia. Meanwhile, the younger Stoneman and two of the Cameron brothers are killed in the war. Ben Cameron is wounded after a heroic charge at the Siege of Petersburg; as a result, he earns the nickname "the Little Colonel." He is taken to a Northern hospital in Washington, D.C., where he at last meets the Elsie Stoneman of the picture he has been carrying; she is working there as a nurse. While recovering, Cameron is told that he will be hanged for being a Confederate guerrilla. Elsie takes Cameron's mother, who had traveled to Washington to tend her son, to see Abraham Lincoln, and the mother persuades the president to issue a pardon to Ben Cameron.
When Lincoln is assassinated at Ford's Theater, his conciliatory postwar policy expires with him. In the wake of the president's death, and with a power vacuum having opened up, Austin Stoneman and his fellow radical congressmen are determined to carry out their desire to punish the South, employing harsh measures that Griffith depicts as having been typical of the Reconstruction era.[16]