In the midst of the American Civil War, Newton Knight, a disillusioned Confederate soldier from Mississippi, becomes increasingly frustrated with the Confederacy's exploitation of poor farmers and conscription policies. After witnessing the horrors of war and the suffering of his fellow soldiers, Newton deserts the army and returns home. There, he discovers that local authorities are confiscating crops and livestock from struggling families to support the war effort. Outraged by the injustice, Newton takes a stand, rallying a group of fellow deserters, runaway slaves, and local farmers to form an armed rebellion against the Confederacy. Together, they establish a small community in the swamps called Jones County, declaring it a safe haven for all those oppressed by the conflict.

As the rebellion gains momentum, Newton and his allies engage in guerrilla warfare against Confederate forces, striving to protect their newfound free state. Throughout this tumultuous period, they face numerous challenges, including internal conflicts and external threats. Newton's defiance also attracts attention from both Union and Confederate authorities. Meanwhile, personal relationships and bonds within the group grow stronger, underscoring their shared vision of a society based on equality and mutual respect.