In the Definitive Edition, the storyline was rewritten by a Native American consultant, Anthony Brave, with some major changes (for example, Crazy Horse is replaced with Chayton's uncle, Uncle Warbonnet, to establish Chayton's personal connections with the Lakota people).
In 1866, Chayton Black, Amelia Black's half-Lakota son whose father died when he was too young to remember, is expanding the Falcon Railroad Company westward along the Bozeman Trail but winds up in the middle of Red Cloud's War. He helps defend the wood trail from the Sioux and becomes friends with Fort Laramie's quartermaster, William "Billy" Holme, an aged Civil War veteran.
Ten years later, in 1876, Chayton returns to the west and again meets up with Holme, now a sheriff, who informs him of a huge amount of gold in the Black Hills of South Dakota. After defending many mining camps from Sioux attacks, Chayton goes to see the Sioux chief Crazy Horse and establish a peace treaty. However, Holme and some of the miners ambush the Sioux before Chayton can begin negotiations, wrecking any chance of peace. Despite the sheriff's warmongering, Chayton still sides with Holme and defends his workers as they gather wood for a new fort. However, once the fort is complete, Holme orders Chayton to destroy a Sioux village without provocation. Chayton refuses and, turning against Holme, allies with the Sioux to destroy the fort, forcing Holme to flee into the hills.
Chayton then convinces the newly arrived General Custer to give him one day to find Holme, who is the real cause of the unrest. Chayton puts on Sioux clothing and blood-red war paint and, joining with Crazy Horse, chases down Holme and confronts him in a mine. Chayton hopes to resolve the situation peacefully, but Holme pulls a gun on Chayton. However, Chayton draws his gun more quickly and shoots Holme, who falls down a mineshaft to his explosive death. Chayton then tries to convince General Custer not to attack the Sioux, but Custer refuses and demands that Chayton choose sides: the United States or the Natives, saying that he can no longer sit on the fence. Chayton agrees, bidding Custer goodbye and siding with the Sioux. He helps gather the Sioux and Cheyenne nations and fights with them at the Battle of Little Big Horn.
After the battle, Amelia Black narrates that she never saw her son again, but she has heard that Chayton was either killed at the Battle of Wounded Knee in 1890, taking a dozen cavalrymen with him, or lived out his days in the Black Hills with his wife and children.
The Definitive Edition makes a number of changes to the story, while keeping the scenarios and gameplay from the original campaign mostly intact. The following changes were made to the campaign for the Definitive Edition:
- Many enemy factions in the first four scenarios have been replaced with outlaw and mercenary units (European-style units).
- The opening section of gameplay for the fifth scenario is now skipped, giving the player immediate control of a Lakota camp.
- Chayton's Lakota ancestry is more heavily focused on, particularly with the role of Crazy Horse being replaced by Chayton's uncle, Frank Warbonnet. Conversely, Amelia's role has been reduced to being mentioned in the narration, and she does not make a physical appearance.
- Backstory has been introduced stating that Chayton and Billy Holmes were once comrades during the Civil War. As such, the two are more familiar with each other in the first two scenarios than in the original game.
- The Red Cloud War storyline has been replaced with a rise in outlaws that threatens both Fore Laramie and the native tribes. The threat on the mining camps has also been changed to feature a new band of outlaws that rose between Chayton's visits.
- Chayton's purpose in meeting with the Lakota is now related to his family, rather than the war between the settlers and natives. He initially seems to want to wash his hands of the settlers' greed to focus on finding his relatives, and only becomes involved in the war when he realizes who is behind the breaking of the truce.
- After the final battle against the United States forces, Chayton tells his uncle that he plans to leave both the tribe and the Falcon Company behind, implying he is disappearing to go on a journey.