In 1906, John was badly wounded in a botched bank robbery. John took this as an opportunity to abandon his life of crime after it abandoned him, as John often puts it. He left with Abigail and Jack, moving them to a ranch on Beecher's Hope to try and start over as ranchers and give Jack a better life.
At some unspecified point in 1911, Jack and his mother were taken hostage by Edgar Ross of the Bureau of Investigation to an unknown location in order to extort John to kill or capture his old gang members. After John had completed his task, Jack was released along with Abigail, and they headed back to the ranch where they were reunited with John. After his parents commented on how Jack had been troubled "growing up without a father", Jack began to finally share some time with John, as he was taught how to hunt and skin Elk, herd cattle, and become a better overall ranch-hand.
Wanting to prove that he was not a child anymore to his father, Jack rode off alone to hunt a Grizzly, despite his father's previous warnings not to head off by himself. Uncle, after failing to prevent Jack from leaving, reported what had happened to John shortly after. John then traveled to the top of Nekoti Rock where he found Jack badly injured and the grizzly bear that had caused the wounds. Saving Jack from the beast, they both rode back to Beecher's Hope, with John disappointed in his son's behavior. Although Jack survived his encounter with the Grizzly, he was scarred with bear scratches resembling those of his father.
Near the end of the story, the ranch was attacked by the U.S. Military as instructed by Edgar Ross, who believed that eventually John must still pay for what he had done. Before the attack, John told Jack to keep himself and Abigail inside the house and to lock all the doors and windows. After initially hiding inside the house with Abigail whilst his father and Uncle took down the first wave of soldiers, Jack soon came out onto the porch with a rifle and helped fight off the second wave in which Uncle was mortally wounded.
Eventually, after defeating numerous more soldiers, Jack was ordered by his father to retreat alongside his mother to the barn. Once John joined them, Jack and Abigail were commanded to ride far away from the farm to find a place to hide, John stating that he would catch up. With this, John slapped the horse, causing it to run out of the barn and away into the Great Plains. In order to ensure the safety of his family, John stepped outside the front barn doors and allowed his life to be taken by the soldiers waiting there, knowing that the government would no longer terrorize Abigail and Jack.
A few minutes later, Abigail told Jack that they had to return after hearing gunshots. At this point the player takes control of a sixteen year-old Jack riding on his father's horse. Upon arriving at the barn, they witness John lying in a pool of blood, his revolver by his side. After great mourning, they buried John's body atop a nearby hill overlooking the house, a hand made grave stone, possibly made by Jack, marking his final resting place, alongside Uncle.
Three years later, a 19 year-old Jack, who suffers from depression from losing his father and mother in a short amount of time, buried his now deceased mother next to his father's and Uncle's graves. Eager to avenge his father, he then proceeded to Blackwater where he met a Bureau agent named Howard Sawicki at the train station. Jack learns from Sawicki that Ross, the man that had betrayed his father three years earlier, had retired a year ago and moved to a quiet cabin near Lake Don Julio with his wife Emily Ross. Jack traveled to New Austin, hoping to confront the former agent. After reaching a cabin by the lake, Jack learned from Edgar's wife that he had gone on a hunting trip with his brother Phillip in Rio del Toro, Mexico. Jack gave her his thanks and stated that, after hearing her worries for her husband, he was sure Ross would be "just fine". After finding Philip at the hunting campsite, who told Jack that Edgar had gone down to the riverside to shoot ducks. Jack confronted Edgar Ross at the river side with building tension. Jack shared words of anger with the old man by the riverside. Ross stated that he would kill Jack too if he didn't leave, to which Jack responded "I ain't goin' anywhere, old man!" causing Jack and Edgar to have a final showdown. Jack drew his gun first and shot Ross, ending the man's life. Finally, after delivering justice to his father's killer, Jack turned and slowly walked away, leaving what had been done; representing that "Everyone will eventually pay for what they've done". However, this act also placed his own future in danger; by murdering Edgar, Jack was dangerously close to becoming an outlaw himself - the very life that his father had hoped Jack would avoid at all costs.
Jack, from here-on, is the playable protagonist, set in the world during 1914, the first year of World War One, as can be seen on the page of a newspaper in Blackwater. Any unfinished side missions or outfits can be done with Jack Marston. There is an exception to this, as the "I know you" side mission can only be completed with John Marston. However, this side mission does not count towards 100%.