Conflict arises between the government and businesses, ranchers, homesteaders and the railroad, as all of those interests compete with one another for control of Cheyenne, Wyoming, the most important railroad hub in 1867. Meanwhile, the Union Pacific Railroad continues its expansion westward, and Bohannon adjusts to being a husband and new father.

Bohannon abandons seeking revenge for the deaths in his family in order to battle Durant for control of the Union Pacific Railroad. Eva gives birth to a baby that was sired during her marriage to Gregory Toole. Elam proposes marriage to her, even though her post-partum depression weighs heavily on her. The Swede takes up with a Mormon family on their way to Fort Smith and later reveals his true nature.

Bohannon tries to find himself again while continuing to drive the westward expansion of the Union Pacific Railroad, under Durant's leadership. Bohannon takes up with a gang of train robbers, but is turned over to the Union Army and imprisoned. Durant manages to get him pardoned. The railroad construction enters the Sioux territory, where the Swede and a misguided Reverend Cole assist the natives in attacking the railroad. Lily Bell seeks to gain control of the railroad from Durant and mails his accounting ledgers to the government. Army officers arrive to find the town has been attacked by the Sioux. Bohannon helps protect the town, while the Swede strangles Lily to death.

In 1865, former Confederate soldier Cullen Bohannon journeys to the Union Pacific Railroad's westward construction of the First Transcontinental Railroad to seek work and vengeance on the Union soldiers who killed his wife and son. Cullen gets hired by the railroad and supervises an all-black "cut crew", including Elam , whose job is to prepare the terrain for track laying. Through conversation with the railroad foreman, Daniel Johnson , Cullen learns more about his wife's death. But tragedy strikes before the name of her killer is revealed to him. Thomas "Doc" Durant begins his "mad, noble quest" to expand his Union Pacific Railroad westward in order to complete the transcontinental railroad. Lily Bell accompanies her ailing husband, Robert, as he surveys the landscape for the Union Pacific. Robert is killed by the Cheyenne natives, and Lily must cope with being a widow on foreign soil. Reverend Nathaniel Cole baptizes Joseph Black Moon, a Cheyenne, then takes him under his tutelage in the church. Season one ends with Bohannon killing a man he believes was responsible for the rape and murder of his wife only to discover that man was not there at the time, thus killing the wrong man.