During his six-year-old daughter Virgie's birthday party, Captain Herbert Cary of the Confederate Army gets word that Fort Sumter has been fired upon and that war has been declared. The men in attendance get ready to report to their Richmond regiment, and the children are sent home. Virgie asks the black house slave Uncle Billy about the war, and he tells her that he has heard that a man up North wants to free the slaves, although he admits he does not know what that means. After the men parade off to war, the Union troops arrive at the Cary plantation, and Virgie hits the commander, Colonel Morrison, with a rock shot from her slingshot. Although he admires her spunk, he warns her not to use the slingshot again. As he leaves, she tauntingly sings "Dixie." With the plantation in enemy controlled territory, Cary, now a scout for General Lee, has to sneak through enemy lines to visit his family. At the end of one short visit, a Yankee troop led by the gruff Sergeant Dudley arrives looking for him. After the soldiers find the family's hidden food and valuables, and Dudley chases Virgie upon discovering that she has covered her face with boot polish out of fear for what the soldiers would do to whites, Dudley struggles with Mrs. Cary, who is trying to protect her daughter, and he shoves her down some stairs. Morrison arrives, and after ordering the men to return the loot, he sends Dudley to get twenty-five lashes and apologizes to Virgie and her mother. When three gunshots are fired to signal that Cary has safely gotten through lines, Morrison leaves, but not before Virgie hits him with another rock shot from her slingshot. Later, as the battle rages in front of the Cary house, Mrs. Cary and Uncle Billy take Virgie into the woods, where, during a violent rainstorm, Mrs. Cary covers Virgie in her cloak. A month later, Uncle Billy arrives at Cary's camp to tell him that his wife is extremely ill. They return to the plantation where Mrs. Cary, now in Uncle Billy's cabin because the house has been burned down, dies after seeing that her husband will take care of Virgie. After the funeral, the Union troops arrive, and Cary hides in a garret attic. Morrison discovers him, but when he learns that Cary was not on a scouting trip and that he was planning to take Virgie to his sister in Richmond, Morrison, who has a daughter the same age as Virgie, tells Cary where he has left a Yankee uniform at a nearby plantation to be mended and writes him a pass to allow him and Virgie to travel to Richmond. Cary, dressed in the Yankee uniform, and Virgie are questioned as they pass through a Union camp, and Dudley overhears Virgie's voice. Cary whips him, and he and Virgie try to escape in their carriage, but the soldiers surround them. Both Cary and Morrison are court-martialed and sentenced to be hanged. A major, sympathetic to their plight, gives Uncle Billy a letter to take to a judge in Washington, D.C. To procure funds for the train trip, Uncle Billy and Virgie dance in the public square. Uncle Billy and Virgie see President Abraham Lincoln, after the judge writes him about the case, and as the president shares an apple with Virgie, she tells him the story. After she relates that her father instructed her that she was "honor-bound" not to tell anyone in Richmond about what she saw while they were traveling, because of a promise he made to Morrison, the president is convinced that the men are not spies and instructs his secretary, John Hay, to rush a pardon for them to General Grant. Virgie hugs the president. Later, back at the Union barracks, Virgie sings "Polly Wolly Doodle" with the Union soldiers and hugs her two "fathers," Cary and Morrison.