The Civil War is over. The citizens of Columbia, South Carolina, lament the sorrow and horror of the war. Colonel Jonathan Wade, with his aide, Lieutenant Patrick, leads the Northern troops of occupation into Columbia and greets Judge Townsend with kindness, but the Judge's daughter, Celia, scorns Jonathan.
The judge invites Jonathan to his home and describes the residence's beauty before the war and its mistreatment by Sherman's troops. The maid, Nicey, deems Jonathan a good man, but Celia denounces him for not understanding the depth of Southern suffering. Jonathan bitterly reveals his own losses from the war, and the two young people begin to understand one another.
Northern pardon brokers selling citizenship to ex-Confederates arouse the indignation of Judge Townsend. Lucas Wardlaw, a hotheaded Southerner, expresses the resentment for Northern reformers. With the arrival of Enoch Pratt, chief of the Freedmen's Bureau, tensions erupt. An evening party at the Townsends' home disintegrates as the Southern citizens furiously refuse to submit to the Northern reforms preached by a fervent Pratt.
Several months later, during a confrontation with Jonathan, Lucas demands back his old way of life, the way of privilege and slavery. Enoch Pratt insists that Judge Townsend be removed from the bench and that the Radical Republicans should use reform as a means of securing future political power. Jonathan sees the shortcomings of all the extremists' demands.
Celia confesses her love for Jonathan, but Lucas taunts the couple with hints of vigilante reprisals. Jonathan's appeal to higher authority to spare Judge Townsend is denied, and he undergoes an agony of conscience. He announces to the Townsends the Judge's dismissal. Judge Townsend rages violently against Jonathan; Celia, though torn between her love for Jonathan and her father, accepts Jonathan's offer of marriage. Her father renounces her.
At the wedding, Nicey sings a spiritual about the wedding feast at Canaan. The Guardian Knights of White Men's Rights harass Nicey and her friends, but Nicey bravely faces them down. Jonathan and Celia try to shelter themselves from the world with their love.
Jonathan's attempts to remain impartial have only angered both Northerners and Southerners. Pratt accuses Celia of influencing the Colonel and enlists Lieutenant Patrick in a plot to destroy Jonathan. Judge Bell, Judge Townsend's replacement, resigns in disgust at the political corruption, and Jonathan loses his last ally. Pratt tries to provoke Jonathan into insubordination and court-martial, and an order arrives commanding Jonathan to confiscate all of Judge Townsend's possessions. Celia and Jonathan react in anger, fear, and confusion; they yearn for another time and another place where they might find peace. Jonathan decides to desert. Townsend publicly denounces the North, and Jonathan and Celia discover that Lieutenant Patrick has carried out the order of confiscation. Sensing a trap, they plan to escape the country. Suddenly, Jonathan's guards capture three Guardian Knights, Lucas among them, about to burn a torch on Wade's lawn.
In the middle of the night, the full contingent of Guardian Knights arrive to free Lucas, while Union soldiers, led by Pratt and Patrick, also surround the house before attempting to arrest Jonathan for insubordination. Shots are fired, and Jonathan is killed; both sides begin to blame each other. Kneeling by Jonathan's side, Celia silences them, accusing both sides of the murder of a good and decent man. Nicey prays that God accept Jonathan into heaven.