October 1862, Jones County, MississippiConfederate soldiers are marching into a fight as they prepare for the start of the Battle of Corinth in the northern part of the state. The men face off against the Union army, leading to a very bloody fight. On the Confederate side is medic Newton Knight (Matthew McConaughey). He carries the injured to safety and tends to the wounded, getting a very clear picture of the horrors of war. This has left Newton jaded to life on the battlefield.Newton learns that those who own 20 or more slaves are exempt from fighting and get to go home. It makes him more tired and annoyed to be fighting in someone else's war. At night, he is found by a local teenage farm boy named Daniel (Jacob Lofland), who tearfully tells Newton that his family's assets have been seized and he's been drafted to fight. Newton comforts the boy.The following day, Newton and Daniel are fighting together in battle. Daniel is shot, and Newton carries him far away, trying in vain to assure him he's not dying. Daniel passes, and Newton brings his body home to his mother so that he may be properly buried.Newton deserts from the Confederate army and goes home to his wife Serena (Keri Russell) on their farm. He expresses his sentiments to her. Upon his return, he learns of another family whose assets are seized by Confederate soldiers. Newton and Serena's infant son is ill, so he goes to the local road house to find a doctor. Instead, he is referred by Aunt Sally (Jill Jane Clements) to her family's slave, Rachel (Gugu Mbatha-Raw). She tends to the child and helps him feel better.The scene jumps to 85 years later to 1947, where Newton's great-great-great grandson Davis (Brian Lee Franklin) is on trial. He is a descendant of both Newton and Rachel, making him 1/8th black, and for this, he is prohibited from marrying his longtime girlfriend, who is white.Newton visits the farm family whose animals were taken. He gives the mother and her three young daughters rifles and teaches them how to shoot. A trio of cavalry officers arrive, with the head officer stating he is looking for deserters. Newton, the mother, and daughters all have their rifles pointed at him, along with several up in the barn that are hung up from the ceiling but made to look like there are others pointing at the officers. They leave but vow to return.The officers go by Newton's house and sic their dogs on him. Newton is chased by one and is caught as he tries hopping over a fence. He grabs his knife and stabs the dog to death. With Aunt Sally's help, Newton is guided to a swamp and is met by Rachel to a group of runaway slaves led by a man named Moses Washington (Mahershala Ali). Moses treats Newton's leg wound.Since Newton becomes a fugitive, Serena leaves her home with their child. This adds to Davis's case since it was known that Serena left and therefore could not have conceived another child with Newton.Newton and Moses bond among the other runaways, and Newton eventually comes to care for the rest of them as well. Newton helps to break off a metal bearing on Moses's neck. Together, with the other runaways, they arm themselves against the slave catchers who run by their hideout. Meanwhile, Rachel is secretly teaching herself to read as she observes the family's children being taught to read. Newton also develops a personal relationship with her and even teaches her how to shoot.July 4, 1863Vicksburg falls to Union forces and more soldiers desert the Confederate army. The deserters find the swamp and unite with Newton and the runaways. Together, they form a militia against the Confederates, as well as a small community within the swamp, where they grow corn and build shelter. They corner a group of Confederates in the woods with guns after the soldiers find their corn supply and try to make off with it. Newton threatens the lieutenant but decides to let him go.Confederate captain Elias Hood (Thomas Francis Murphy) approaches Aunt Sally in her shop to persuade Newton to disband his group so that they will not carry out hangings among their people. When that doesn't work, the soldiers start burning barns and offering pardons to those in the militia that lay down their arms. Newton then rallies his people to fight back. Four of Newton's people, including two boys, are captured by the soldiers and are hung. At their burial, Newton stirs up the people's emotions to convince them now is the right time to fight back.The militia strikes back by having Moses and a couple other men in coffins spring up at the right moment and fire at the soldiers. A battle ensues, with many soldiers getting hit and killed. Newton follows Hood into the church and corners him under a bench. He shoots his gun at Hood, but never intentionally hitting him. Instead, he strangles him to death and drags his body outside.March 1864, Ellisville, MississippiThe militia takes the battle further toward the Confederates, having grown in size over the months. Eventually, the militia overpowers the army. They take down the Confederate flag and raise the American flag. The people celebrate their victory. Newton brings Rachel into a room where she can have her own bed. She is overwhelmed and starts crying.Colonel Lowry (Wayne Pere) is marching with his men along Ellisville to send a regiment against the militia. Newton gathers everyone and gives them a speech. He reads from a document that states the conditions of what is to be their Free State of Jones.June 1865The militia holds out until the end of the war and continues to thrive. Freedmen are able to cultivate land for themselves. Moses is able to reunite with his wife and child. Three months later, however, the promise of "40 acres and a mule" is rescinded from the freedmen. Still, the people manage to expand their community, including setting up a school where Rachel is teaching people to read.Serena reappears and reunites with Newton and their son, who is now a young boy. She explains how her situation has fared since leaving him, and how her barns have been burned down. Newton invites them to stay with the community.Moses sets off when his son is taken by slave owners. Newton follows him to make sure he doesn't get killed. It is now a year after the emancipation, and slaves are still being worked on the fields. Moses takes his son but is cornered by two slavers with rifles. Newton intervenes and is later put on trial for his actions. He protests the charges against him.In response to these types of laws, Congress puts the South under martial law. Additional Union troops are sent down there, and former Confederates are stripped of their power. The freedmen are allowed to vote for the first time, and so Military Reconstruction begins to take place. A group of freedmen march together as a union in protest down on Ellisville. In turn, the Ku Klux Klan organizes and commits acts such as arson against a church.Rachel gives birth to her and Newton's child. Serena even helps her take care of the child. This is brought to the attention of Davis's case when trying to determine whether or not it was Rachel or Serena that he is descended from. The evidence is made clear with Newton's family Bible that contains written proof that Rachel gave birth.Moses goes around gathering information from freedmen and slaves. He is pursued by a group of angry white folks. Newton later finds all of Moses's papers spread across the ground, until he comes across Moses's body hung from a tree. The community deeply mourns this loss.Election Day arrives, with eyes on Newton and his people marching to vote. When he gets to the voting hall, Newton requests republican tickets. After the vote, it is stated that the democratic vote beats the republican by a huge number.Over the next year, Klan activity rises as Union troops are pulled out. Thousands of African-Americans are murdered leading up to the election of 1876. This makes Rachel worry for her and Newton's child.At the end of Davis's case, he is granted bail on the condition that he get his marriage annulled and that he move out of Mississippi. He refuses to do so, seeing his case as unlawful, and the judge sentences him to five years in prison. However, the Mississippi State Court overturns his conviction to avoid federal issues.The last bit of text states that since Newton and Rachel were unable to marry, he deeded her 160 acres of land, making her one of the few African-American women to own land. They would live on that farm for the rest of their lives.