Inspired from true life, this period war drama is set against the backdrop of the American Civil War and revolves around Newton Knight, who revolted against the Confederacy and the lead and armed revolt after declaring Jones County, Mississippi a Free State. If
After surviving the 1862 Battle of Corinth and being told of the Twenty Negro Law, Newton Knight, a poor farmer from Jones County serving as a battlefield medic in the Confederate Army, deserts and returns home to his farm and his wife, Serena, after seeing his nephew Daniel get shot and killed. While there, he befriends Rachel, an enslaved woman who has secretly learned to read.
Newton's disenchantment with the Confederacy grows after finding out that troops were taking crops and livestock for taxes. After helping one family resist such a raid, he is pursued by Confederate agents and bitten by an attack dog. With the help of abolitionist-oriented Aunt Sally and multiple slaves, he escapes to a swamp where some runaway slaves led by Moses Washington tend to his wounds.
After the Siege of Vicksburg, many Confederates abandon their post, and many of them end up at the swamp, where Newton becomes their captain. The ex-Confederates and runaway slaves form a revolt against the Confederacy. They raid Confederate convoys and capture a piece of south-east Mississippi, organizing it as the 'Free State of Jones'. Despite getting little help from the Union, they manage to hold out until the end of the war.
Newton continues to fight racial inequality after the war. He helps free Moses' son from an 'apprenticeship' to Rachel's former master. After Moses is lynched while registering freedmen to vote, Newton participates in a march of voters to the polls.
Newton and Rachel have a son, Jason. Since they are unable to legally marry, Newton arranges to deed a parcel of land to her.
The story is interspersed with the story of Newton's great-grandson, Davis Knight, who is arrested under Mississippi's miscegenation laws in 1948. Since he is possibly of one-eighth black descent, under Mississippi law at that time he is considered black, and therefore could not legally marry his long-time sweetheart. He is sentenced to five years in prison, but his conviction is thrown out by the Mississippi Supreme Court in 1949, rather than risk the law being declared unconstitutional.