Washington, D.C. 1865. A man heads into a church and confesses to the priest about things he did during the war, saying they were evil, unspeakable things. He says the devil had taken over him. The man says he cannot confess the sin though, they are too horrible to confess. The priest asks about another man, but the priest turns out to be Cullen Bohannon. He shoots the man in the head and heads out of the church.
Thomas "Doc" Durant pitches his idea of the transcontinental railroad to skeptical listeners. He tries to drum up some support and funding. Durant eyes one man in the room and then later explains his business proposition. He owns the main construction company that currently builds the railroad. Essentially, Durant is paying himself with government subsidies. The man (a senator) initially declines unless Durant agrees to give him 400 shares. Durant argues that he could move the construction away from the senator's 50,000 acres of land, affecting the future division and sale of it. Now the man concedes, but Durant haggles him down to measly 100 shares instead of the original 200 proposed.
Meanwhile, on a train, two young brothers, Sean and Mickey McGinnes, learn of murder at the church and Cullen just happens to be in front of them. The two are heading west to look for work on the railroad. Cullen says he is as well. They enter Council Bluffs, Iowa where the railroad abruptly ends. A flurry of activity is seen: men are blasting the way through the hillsides, men are jumping off the train to see where they can apply for the jobs. Cullen finds the equivalent of human resources and applies for any job the man has. The man, Daniel Johnson asks if Cullen kept slaves. Cullen says yes and becomes the supervisor of a construction crew full of African Americans. Elam Ferguson is one of them and he is not too pleased about it. A priest performs a baptism on Joseph Black Moon.
Planners advise Durant on the latest path through the land. Durant argues that the railroad path is too straight and in order to make more money he wants the tracks to curve even though the land is flat. Durant gets $16,000 per mile. He quickly fires the master planner and has the younger one take over. Out in Nebraska territory, a man (Robert) checks elevation while a woman (Lily) holds an elevation marker. Robert appears to have become ill as of late and advises Lily to go to Chicago when it is all over. They embrace for a long while. Later that night, in the tent city set up along with the railroad, Cullen meets some of the other white men. Cullen says he owned fives slaves (two of them women) but that he freed them one year before the war started. His wife had convinced Cullen that he needed to free his slaves. Cullen explains that she is now dead but not because of the war itself. Daniel Johnson listens.
In a tent, Robert again tells Lily that the cough is worsening. Lily prefers to ignore this. The next morning and nearby, Native Americans shoot arrows into a railroad worker. The one into his throat kills him. All of a sudden the natives start attacking people in their tents. Robert tells Lily to run into the forest and Robert follows. One Native follows them, slowly tracking them. Robert has a fit of coughs and can't go on any further. The two kneel and stay quiet but the cough gives away their location. The Native shoots an arrow at Lily and one pierces her in the hand. Robert saves her by attacking the native but he is stabbed by a large knife that the native also has. Lily removes the arrow and uses it to kill the native. However, Robert is now dead and she continues into the forest without him.
The next day, Daniel Johnson wakes up Cullen, who appears to be suffering from a major hangover. The diggers continue hacking at the dirt, making a path so that the track can be laid. Elam and another railroad worker start singing to get through the day. Cullen doesn't appear to mind. Durant receives a Morse code message and it says that Robert is dead. Durant obviously knows this man and sends a message to Union Pacific saying he needs to head out to "Hell on Wheels" the town that travels with the construction unit. Elam helps a coworker get some water before he faints. Cullen notices them drift away but then understands that they were just getting water. Cullen was just about to correct Elam from referring to him as "master". However, Daniel Johnson isn't so understanding, he whips Elam's coworker (Willie) and then has his horse kick him in the face.
Later on Cullen visits Elam and sees how Willie is doing. Elam is sharpening his knife to stab Johnson but Cullen tries to talk him out of it saying nothing good will come out of it. Elam argues that things have not changed, even though the slaves were freed. Cullen says to let go of the past, but Elam challenges him, saying "have you let it go?". The McGinnes brothers are seen putting on entertainment shows to make some money.
Johnson asks Cullen more about the war, but Cullen stays quiet, saying he doesn't like to talk about it. Johnson mentions that he did cross lines of morality he never thought he would have during the war. Cullen argues that moral men do not cross the line but admits he did plenty of things he was ashamed of in the war. Cullen asks Johnson about going to Meridian, Mississippi, but Johnson pulls out his revolver and aims under the table. Pulling Cullen outside, Johnson says he knows about the two men he killed in addition to the man at the church. Johnson knows about Cullen's wife. But Cullen says that Johnson was the one that did it to her. Johnson still has his revolver out, but mentions that the sergeant was the one that hanged her, saying that she did not kill herself. But before he can get the name of the sergeant, Elam cuts into Johnson's neck and kills him.
Durant laments that this business is not for the faint of heart. As he monologues, Joseph Black Moon surveys the damage at the site where Robert was killed. Lily wonders onwards past the forest. Images show the travelling town moving forward, leaving behind scars on the earth. But Durant powers on in order to continue making money. He may seem greedy he says, but without men like him, the railroad would have never been built.