Cold Mountain opens with its protagonist, Inman, lying in a Virginia hospital recovering from war wounds. He is shattered by the violence he has witnessed while fighting in the Confederate army and wants to go home to reunite with Ada, the woman he loves. Inman talks to a blind man and realizes that losing something you already have is worse than not getting what you want. One day in town, Inman writes to inform Ada that he is returning home. That night, he leaves the hospital through a window and sets out on his journey back to North Carolina.
The story of Inman’s adventures intertwines with Ada’s story. Ada is left alone to manage Black Cove Farm following her father’s death. She is bereft and has no idea where she belongs or how she should earn a living. When she visits the Swangers, her neighbors, Ada looks into a well to foretell her future. She sees a man walking through the woods on a journey but does not know what this vision means. The next day, Sally Swanger sends a local girl named Ruby to help out on the farm. Ruby and Ada become friends and establish a comfortable domestic routine.
Meanwhile, Inman’s journey westward is fraught with danger and violence. He is pursued across the Cape Fear River, escaping with his life thanks to the skill of a girl paddling a dugout canoe. Inman intervenes when he finds a dissolute preacher, Solomon Veasey, attempting to murder his (the preacher’s) pregnant lover. The preacher is exiled from his community, and Inman is forced to -continue part of his journey with Veasey. Inman has to intervene again when Veasey causes trouble in a store and at an inn. While Veasey spends the night with a prostitute called Big Tildy, the peddler Odell tells Inman a sad story about landowners’ cruelty towards slaves.
The next day, Inman and Veasey help a man remove a dead bull from his stream. This man, Junior, invites them to his home to spend the night, and several strange things happen. Inman is drugged and forced to marry Junior’s wife, who the author suggests may be a cannibal. Junior then hands Inman and Veasey over to the Home Guard, the military force that has been searching for Inman. Inman is forced to walk eastward, retracing his steps. The guards decide to shoot the men and bury them in a shallow grave. Although Inman escapes with a slight head wound, Veasey dies.
Ada’s story resumes. The novel follows her adjustment to a life of labor in harmony with nature. Ada’s friendship with Ruby blossoms as she begins to identify with the natural world. The female protagonist lays down roots at the farm and recalls memories of Inman and her father. Occasionally, she finds herself touched by events surrounding the war. A group of pilgrims forced into exile by Federal soldiers seeks shelter for a day at the farm. Ada recalls Blount, a soldier she met at a party in Charleston who later died in battle.
Finally, when Ada and Ruby visit the town of Cold Mountain, they hear a story told by a prisoner jailed for desertion. The captive tells of the sadistic Teague’s band of the Home Guard. On their walk home, the two women observe some herons, and Ruby explains that a heron fathered her. Ada tells the intricate story of her parents’ relationship and her mother’s tragic death in childbirth. Ruby’s father, Stobrod, appears later, caught in a trap the women have laid to catch a corn thief. He explains that he is living in a mountain cave with a community of outliers who object to the war. Stobrod plays his fiddle to prove that he is a changed man, but Ruby remains skeptical.
Inman’s story continues. Having been dragged from the shallow grave by wild hogs, Inman meets a kind slave who feeds and clothes him and draws a map of what lies ahead. He returns to Junior’s house and kills him. Inman then continues on his journey, full of despair, a “traveling shade.” Inman meets an old woman who offers him shelter at her camp in the mountains. He rests and regains his strength while the woman nurses his wounds and talks about her life. Inman learns that the woman ran away from a loveless marriage and raises goats for company and sustenance. Inman identifies with the goat-woman, but concludes that he could not live such an isolated life.
Inman continues to wander and meets a man called “Potts,” who directs him to a cabin belonging to Sara, a kind young woman whose husband died in battle. Sara feeds Inman, mends his clothes and tells him her story. Despite her bravery, she is close to despair. The next day, Inman kills three Federal soldiers, called “Federals” in the novel, after these men threaten Sara and her baby and steal the family hog, the only form of sustenance that the family has.
At home, Ada and Ruby start harvesting apples as autumn nears. Stobrod reappears with a slow-witted banjo player named Pangle. Ruby’s father asks for shelter at the farm and for food provisions, explaining that the men intend to leave the outliers’ cave because it is getting too dangerous. To Ruby’s annoyance, Ada agrees to help Stobrod. The men go off into the mountains with a boy from Georgia to find their own camp. Teague’s Home Guard appears looking for the mountain cave and shoots Stobrod and Pangle. The Georgia boy, who survived because he hid in a thicket, runs to the farm and tells the women what happened. Ada and Ruby leave to bury the bodies and camp out in the mountains. The next day, they bury Pangle but discover that Stobrod is still alive. Ruby removes the bullet from her father and takes him to an abandoned Cherokee village.
Meanwhile, Inman reaches Black Cove Farm and finds himself in sight of Cold Mountain. The Georgia boy tells him that the women have left to bury Ruby’s father. Inman climbs the mountain and finds Pangle’s grave but loses Ada’s tracks in the snow. The next day he hears a gunshot and finds Ada hunting turkeys. The lovers spend four days together at the Cherokee village, discussing their feelings, past experiences, and plans for the future. They decide that Inman will walk north and surrender to the Federals, since the war will be over soon. On the fifth day, Stobrod is strong enough to travel. Ada and Ruby leave for the farm and the men follow.
On the journey back to Black Cove, the Home Guard ambushes Inman and Stobrod. Inman kills all the men except for Birch, Teague’s second-in-command. Birch seems powerless and scared, but he shoots Inman before the Inman can attack him. Ada hears the shots, finds Stobrod, and races back to locate Inman. She holds him in her lap as he dies.
In a brief epilogue set ten years later, Ada, her nine year-old daughter (presumably by Inman), and Ruby’s family gather in the evening. Ruby has married the boy from Georgia, called Reid, and has had three sons with him. The family sits down to eat. When the meal is over, Stobrod plays his fiddle and Ada reads to the children.