She is first seen on the train from Blackwater. It is unknown why, but she is possibly visiting her one surviving brother or getting supplies for her ranch. She reveals she was on the train when she says "I saw you get on the train in Blackwater, you and those gentlemen in bowler hats". Bonnie rescues John after he is seriously wounded in the initial confrontation with Bill Williamson at Fort Mercer by a rifle shot to the chest. Bonnie pays a doctor $15 to heal Marston's wounds and provides lodging in return for assistance with ranch duties on the MacFarlane's Ranch. John does several missions at the ranch, such as herding cattle and breaking horses. After finding out that John is at the ranch, Bill Williamson's boys set the ranch's barn on fire and John risks his life to rescue the horses out of the burning barn. Bonnie is later taken hostage by members of Bill Williamson's gang, who threaten her life unless Marston and the Marshall release Norman Deek from the Armadillo jail in Hanging Bonnie MacFarlane. After traveling to the ghost town of Tumbleweed and attempting to hand the man over, it is revealed to be an ambush. The gang attempts to hang a brutally beaten Bonnie, but the rope tightens around the side of her throat, preventing her neck from being broken. John then shoots down or cuts the rope she is hanging from and she survives. Marshal Leigh Johnson takes her back to Armadillo after all of Williamson's men are killed.
After the death of Dutch van der Linde and he recovers his family, John returns to MacFarlane's Ranch and visits Bonnie to purchase cattle. Shortly after, Bonnie calls upon John by telegraph to bring the ranch some corn to make up for corn lost to pests at their ranch. After John and Abigail Marston leave the ranch, she gazes longingly after the couple, shuffling her feet as she watches the wagon leave. She then turns to Amos as he walks into the general store and then follows him in, marking her last appearance in the main storyline. It is suggested by Abigail that Bonnie had developed feelings for John as they ride back to Beecher's Hope. The way in which she stared at the two as they left also greatly indicates this.