In a flashback to 1863 Virginia, a youthful Thor Gundersen plays harmonica and sings with fellow Union soldiers around a campfire. Their revelry is interrupted when a band of Confederates rides into the camp and slaughters the soldiers. Thor's friend, Goodwin, takes a bullet to the leg. Thor runs into his own tent and struggles to load his gun. "Please," he pleads with the Confederate who enters and points a rifle at him, "I am only a quartermaster." When the Confederate's gun misfires, he knocks Thor unconscious with the rifle instead.
Imprisoned with Goodwin in Andersonville after their capture, Thor is starving and filthy. He digs through the rubble and unearths his harmonica box. Very gently, he blows a note. A Confederate guard hears and orders Thor to play a song. Thor resists. The guard slips a knife inside Thor's upper lip and orders "the Swede" to play. Thor balks, proclaiming, "My name is Thor Gundersen from Norway." The guard slits Thor's lip and walks away with the harmonica.
Later, the guard catches Thor sharing his meager slop with Goodwin and lashes Thor repeatedly. One night, Thor awakens in horror to Goodwin gnawing on his arm. Thor pushes Goodwin away, but he snarls and lunges for more. Thor shoves Goodwin's face into the mud, killing his only friend to save himself. He has become the Swede.
Naomi sings to William on the Hatch homestead as Isaac chops wood. She hears the chopping stop and brings a pitcher of lemonade outside. As she approaches the shed where her sister, Sara, is working, apples tumble out the door. Sara turns toward Naomi, clutching her bloody stomach, and collapses. Naomi grabs a rifle and shouts for Isaac to get William. She searches for her father and finds him stumbling out of the barn with an axe in his back.
Naomi turns and runs, past Isaac's lifeless body, back into the house. She bars the bedroom door just as the Swede starts slamming into it. Shaking, Naomi loads her rifle and fires at the door. "Naomi," the Swede sings, "I'm coming to get you." Naomi grabs William and climbs out through the window as the Swede chops down the door. The Swede catches Naomi's hand as she reaches back for her rifle. "You best run," he advises. Naomi flees as the Swede sees Cullen flying down the hill towards the house.
Cullen passes the dead Hatches and sees the Swede chasing Naomi into the woods. The Swede follows the sound of William crying. Cullen runs after them, yelling, "Naomi! I'm coming!" Naomi reaches a creek and hides in the roots of an overturned tree on the water's edge, frantically trying to quiet the baby. Cullen approaches above them and hears William. He looks down just as the Swede shoots him in the leg. Cullen tumbles into the creek and floats, face down, blood pooling around him. Naomi grabs Cullen's gun and fires at the Swede as he runs across the creek towards her. Suddenly, Cullen leaps up and wrestles the Swede into the water, holding him under until he stops fighting back. On the brink of death, the Swede smiles up at Cullen. Cullen releases him. The Swede gasps, still alive. Cullen picks up a rock and knocks him out.
At the Hatch homestead, Isaac stares at Aaron and Sara's corpses, his own head heavily bandaged. The Swede blinks into consciousness, chained to the water pump.
In the shed, Naomi sutures Cullen's wound. He's lost a lot of blood and needs a doctor. Cullen plans to see one at Camp Douglas -- he's bringing the Swede there because it has jurisdiction over all crimes committed in the Utah territory. Cullen promises that the Swede will hang, but Naomi encourages him to "end it here." Cullen shakes his head.
Cullen follows the Swede on horseback, his rifle pointed at the Swede's back. The Swede asks why Cullen didn't kill him earlier, supposing it's because Cullen wants to end things the way he believes it should have ended "a long time ago upon that trestle bridge." However, the Swede says, "Heavenly Father has spared my neck twice now. He can manage a third."
The Swede chatters as they ride, reminiscing about Andersonville and how much Goodwin suffered after being shot in the leg.
Lying tied to a tree trunk, the Swede watches Cullen limp around the campsite, gathering wood for a fire. The Swede reaches for a sharp rock on the ground, but he's interrupted by an approaching rattlesnake. Cullen grabs the rattlesnake and dangles it in front of the Swede's face before cutting off its head.
Cullen eats the rattlesnake for dinner. The Swede observes that Cullen would rather be with him instead of with family. The Swede suggests Cullen fears killing him. Cullen stares at the Swede and declares, "I fear it would bring you peace." The Swede points out that if he hangs for his crimes, Cullen must hang for his own. The Swede sleeps as Cullen stands guard.
In the morning, Cullen probes his painful leg wound. He uncaps two bullets and pours their gunpowder onto his leg. He touches a burning branch to the gunpowder, cauterizing the wound, and screams. The Swede uses the distraction to grab the sharp rock.
Cullen is in bad shape as they ride through the desert. The Swede covertly uses his rock to saw at the tether between his horse and Cullen's.
When Camp Douglas is in sight, the Swede hops down off his horse, refusing to go any further. He challenges Cullen to hand down his final judgment "as God planned" right there in the desert. The Swede plunges his rock into Cullen's wound. He wraps his shackles around Cullen's neck, choking him as they fall to the ground. Cullen fumbles for his gun. He misses twice before finally shooting the Swede in the side.
Delirious and screaming in pain, Cullen drags the Swede's body towards Camp Douglas. He fires into the air, then passes out. The Swede rises, grabs the gun, and points it at Cullen's head. "Thank you, devil," he whispers, but he doesn't pull the trigger. Four U.S. Cavalry soldiers surround them. The Swede collapses.
Cullen screams as a doctor removes bullet shards from his leg.
Awakening after four days in recovery, Cullen throws back the blanket to reveal his leg -- still attached. The doctor explains that the bullet shattered and Cullen had shrapnel all through his thigh; some deeper fragments couldn't be extracted. He tells Cullen that the Swede has been tried and sentenced.
In jail, the Swede hears a harmonica and calls to the guard playing it. The Swede tells him it's the most intimate instrument: " The best players, for a moment, they touch God." The Swede reaches for the harmonica and offers to show him, but the guard walks away.
Cullen approaches unsteadily, using a cane. The Swede begs Cullen for mercy, betraying his fear of hanging, and asks Cullen to put him out of his misery. The Swede admits he was wrong -- Cullen is not the devil; he is just a man of war. "Forgive me," the Swede whispers, "Forgive yourself." Guards arrive and take the Swede to the gallows.
In the yard, the Swede's sentence is read aloud. His arms and legs are bound, but he refuses the hood. He looks directly at Cullen as he speaks his last words: "I am Thor Gundersen, from Norway." The Swede is hung.
Cullen leads his horse out of Camp Douglas. He cuts away the splint on his leg, flexes it gingerly, and hobbles forward.