Cold Mountain is the story of a wounded Confederate deserter's return to his home and the city girl who learns to live there on a farm with the help of a tough, capable, and independent mountain girl.

A gravely wounded Confederate soldier, a veteran of the savage Battle of Fredericksburg, writes from the hospital to the woman he left behind that he is coming home to her. Inman deserts, knowing that Home Guards are on the prowl for deserters, and he begins a long trek westward to Cold Mountain, where he grew up. Inman's youth has filled him with respect for Indian lore, and warfare has filled him with nightmares of shattered bodies and incompetent leadership. Having enlisted to protect his homeland from invaders, Inman is disillusioned by humanity's brutality and has no loyalties. Inman worries that 4 years of horror have transformed him into a monster his would-be spouse on idyllic Cold Mountain, Ada Monroe, cannot love.

Ada struggles to survive in the shadow of Cold Mountain at Black's Cove after her father, Monroe, a Charleston preacher, moves there for his health but suddenly dies. Ada has enjoyed a protected, comfortable life but been denied training in anything practical. Snobbishly prickly, she is an object of mirth among the locals but is befriended by Ruby, a troubled young woman who has learned survival through trial and error, having been all but abandoned by her worthless father, Stobrod. Stobrod has enlisted and is presumed dead or deserted, so Ruby is available to help and tutor Ada. They become fast friends and Ada gradually becomes a more rounded person, who is able to survive.

As Inman walks home, he encounters a number of colorful characters. A failed preacher, Solomon Veasey, becomes his companion for a way, until they are seized by the Home Guard and dragged back eastward. The guardsmen tire of dealing with their charges and summarily execute them, but Inman survives, wounded in the head, and resumes his journey home. Gypsies; an aged woman, living as a hermit, tending goats, drawing pictures, and selling patent medicines; and several helpless women put upon by fate and the evils of mankind cross Inman's path. Exhausted, disillusioned, and worried about meeting Ada, Inman reaches Cold Mountain alive, fasting in the event Ada rejects him, because that will gain him entry to the land of peace the Cherokees claim lies hidden inside the mountain.

Stobrod and an innocent dull-witted, musical companion show up at Ada's farm, re-igniting Ruby's bitterness about her lost childhood. Ada convinces her to leave them provisions at a secret location on Cold Mountain (but not harbor the fugitives) and there the Home Guard, led by Teague, discovers them. After making them entertain them, the guardsmen shoot them down in cold blood. The women learn about this from an eyewitness and set out through deep snow on a grim burial detail. Stobrod has survived, badly wounded, and they nurse him back to health. Inman learns about all of this from that same eyewitness and heads to the spot. He and Ada are united, talk through their concerns about what the past has done to them and look forward to a happy future after the war. The men and women divide for the trip home, and Teague confronts Inman and Stobrod. Stobrod escapes and Inman kills all but one of the guardsmen and is trying to talk him into laying down his rifle and walking away when hapless Birch fires a lucky shot and fells Inman. Ada follows the sounds of gunfire and cradles Inman as he dies. Ada is pregnant with his child, and we see, 9 years later, Ada, her daughter, Ruby, her husband (the Georgia boy who is the eyewitness), their three rambunctious sons, and a fully reformed Stobrod, making a successful, happy life together in the shadow of Cold Mountain.