The Union Pacific struggles onward without Cullen Bohannon, who is presumed dead after his abduction. Durant forces new chief engineer Martin Delaney to attempt to traverse a frozen river, but the train sinks. Durant uses Mickey to recoup his lost money.
General Ulysses S. Grant sends Reconstruction leader John Campbell to Cheyenne to restore order to the Union Pacific as provisional governor of Wyoming.
Naomi gives birth to a boy, William. Before they can leave for Cheyenne, a wounded Major Bendix approaches the fort and asks for shelter. The Swede turns Bendix away, believing it’s a trap arranged by Cullen.
Mickey finds Eva unconscious after being raped. He attempts to assault her further, but she shames him into stopping, then uses that leverage to get herself a job at the casino.
Campbell and his men, Jessup, Atwood, Judge Webber and Heckard, announce their presence in Cheyenne by holding a kangaroo court for a murder suspect and hanging him. This sparks a power struggle between Durant and Campbell for control of Cheyenne.
On his way out of Fort Smith, Cullen tricks The Swede into publicly confessing to the murder of the real Bishop Dutson.
Cullen returns to Cheyenne with Naomi and William, and learns Elam has disappeared after going out to search for him.
Durant refuses to reinstate Cullen as chief engineer. They disagree on how best to advance the railroad past Sherman Peak. Cullen gets a job working as a railroad laborer with the freedmen.
Jessup and Heckard beat Cullen unconscious. Naomi tends to his injuries and tries to get him to rest, but Cullen insists on continuing to work.
Against Delaney’s wishes, Durant allows Cullen to assess their options for getting past Sherman Peak.
Naomi overhears Ruth gossiping about Mormons. Later, Ruth comes to Naomi’s tent to apologize, but ends up further antagonizing Naomi.
Jessup throws Mickey in jail, and Mickey cedes control of the casino to Campbell in exchange for his freedom. Later, Mickey strangles Jessup in an alley.
Elder Moss hesitates to hang The Swede for impersonating a bishop. Aaron Hatch promises proof that The Swede is an impostor from the head of Dutson’s ward. When a telegraph from the ward arrives, The Swede suggests it’s been falsified. He proposes a solution: bring Brigham Young to the fort to make the final decision.
Cullen warns Durant that Campbell won’t stop at the casino, and will try and take over the railroad too.
Naomi fights with Cullen over his lack of family responsibility. He promises to attend church with her, but gets caught up in railroad work and misses Mass.
In Mexico, Sidney Snow escapes being hung by Marcos Fuentes. Sidney travels to Cheyenne, where he recognizes “Colonel Bohannon” from the Civil War. They reminisce about the past until Cullen becomes uncomfortable with Sidney’s strongly-Confederate perspectives.
Marcos tracks down Sidney in Cheyenne, and a shootout ensues. Sidney kills Marcos, as well as a small boy. Sidney nearly shoots Naomi as well, but Cullen intervenes just in time. Sidney is arrested.
Brigham Young spares The Swede, acknowledging the progress the Mormon spur line has made under his leadership. Later, The Swede confesses his true past to Young.
Heckard sneaks into Durant’s train car, accuses Durant of killing Jessup, and beats him unconscious. Cullen finds Durant the next morning, stitches him up, and convinces him to take the railroad over Sherman Peak, rather than around or through it. Maggie Palmer lends Cullen the money to buy a steam dredge, which Cullen plans to convert into a rock shovel.
Aided by a Comanche medicine man, Elam slowly recovers from being mauled by a bear. The tribe names him “Bear Killer.” Jimmy Two Squaws recognizes Elam and tries to force him to leave, but Elam kills Jimmy instead. Later, Elam and some Comanche braves attack Major Bendix and his men. After returning from battle, Elam kills another brave and rides away from the Comanche camp with slave women in tow.
Durant confronts Campbell about Heckard’s attack. Campbell agrees to put Heckard on an afternoon train back east. Durant boards the same train. After the train leaves Cheyenne, Durant has Heckard ejected from the train, then bludgeons him to death.
Elam follows the railroad tracks to Cheyenne, looking to sell his slaves. Cullen hears that Elam is approaching and rides out to meet him, but Elam doesn’t recognize Cullen. Realizing that Elam “ain’t right,” Cullen tells him to wait outside town until Cheyenne’s auction house opens. Cullen brings Eva out to Elam, but Elam doesn’t recognize her either.
A crowd gathers and jeers as Elam tries to sell his slaves. Cullen tries and fails to jog Elam’s memory. They fight, and Cullen shoots and kills Elam. Cullen buries Elam’s body and weeps.
Naomi takes William and leaves Cheyenne. Cullen catches up to them and joins them on the ride back to the Mormon fort. When they arrive, Aaron Hatch tells them “Bishop Dutson” has gone to Utah with Brigham Young. The next morning, Cullen returns to Cheyenne without his family.
Campbell grants Sidney his freedom in exchange for Sidney going to work for him as marshal. Sidney’s first assignment is to find and arrest all bail-jumpers, fugitives, and indentured freedmen, which results in the roundup of most of the Union Pacific’s labor force, including Psalms. The men are told they’ll be shipped out of town and returned to the various jurisdictions where they committed their crimes to stand trial. Durant is also arrested, for Heckard’s murder. Mickey escapes capture by running into the church, where Ezra hides him under some floorboards.
Cullen asks Sidney to release the workers. Sidney sends Cullen the jail keys with a message: “You want the men, come get ’em.” Cullen doesn’t take the bait, and instead recruits Mickey to help break the men out.
Campbell and Louise begin a romantic relationship.
Mickey allows himself to be arrested while buying ammunition and guns. Sidney tortures him, and Mickey says Cullen is planning to attack as the men are loaded onto the train, but the story is a lie. Mickey smuggles a handcuff key into the cell.
As the prisoners depart the jail to be loaded onto a train, they unlock their handcuffs while the guards aren’t looking. Cullen sneaks onto the train and disconnects the prisoner car from the locomotive, where Sidney is riding. A shootout ensues, and Sidney escapes. Upon returning to Cheyenne, the men head inside the church and refuse to work until they are assured no one will come after them.
Collis Huntington meets The Swede while negotiating with Brigham Young for Mormon workers. The Swede offers to accompany Huntington’s new Mormon workers, but Young refuses to let him go. Later, The Swede murders a man who insulted Young and refused to make a deal with him, and coerces the man’s brother into doing business with the Mormons. The Swede then asks again to join the Central Pacific workers, and Young consents.
Cullen takes over Sidney’s marshal position under Campbell in exchange for Campbell’s protection of the rail workers. Meanwhile, Sidney barricades the church doors, sets the building on fire, and shoots at anyone who tries to get out. Cullen and Durant help the workers escape, but the church is destroyed, and Ezra burns to death after hiding under the floorboards and becoming trapped.
The next day, Sidney rides through Cheyenne and calls out Cullen. Ruth, devastated by Ezra’s death, shoots Sidney twice. Cullen tries to save Sidney’s life so Ruth won’t be tried for murder, but Sidney dies.
Ruth pleads guilty to murder, rejecting Campbell’s offer of a pardon and Cullen’s efforts to change her mind. The night before her execution, she confesses her love for Cullen. The next day, she’s hung from a gallows built in the town square.
Louise prints an article about Ruth’s hanging that paints Campbell in a negative light. He ends their relationship and destroys her printing equipment.
A telegram from now-President Grant acknowledges the judicial system Campbell has established in Cheyenne and removes the “provisional” from Campbell’s governor’s title. With Major Bendix and his men in town to support him, Campbell orders Mickey and his cohorts out of Cheyenne. Mickey takes his working girls with him, and Eva goes along after negotiating a position as their madam.
Cullen watches the completed steam shovel successfully lift a large pile of rocks. He walks into Durant’s tent and declares, “I quit.”
Cullen goes back to Fort Smith and finds it deserted after what appears to be an Indian attack. He discovers a badly injured Elder Moss, who points west and whispers “Naomi” before dying.
Cullen rides to Salt Lake City, where he learns that Fort Smith was hit by smallpox. He finds Mrs. Hatch on her deathbed, who tells him Naomi and William survived but refuses to say where they are, telling him only that they’re “further west.”
Cullen meets with Collis Huntington, who knows Cullen has left the Union Pacific. He promises to help Cullen find his family in exchange to coming to work for him. After initially rejecting Huntington’s offer, Cullen follows him to California and signs up for rail work on the Central Pacific, along with a 1.5% share of the company.