John Marston, a former outlaw, is sent by the Bureau of Investigation - a precursor to the modern-day FBI - to capture his former brother in-arms, notorious criminal Bill Williamson. Throughout his adventures in New Austin, Marston allies himself with several figures.
The Man from Blackwater sees John Marston teaming-up with Marshal Leigh Johnson to take down Bill Williamson and the Williamson gang. Over the course of the movie, Marston works with Marshal and his two deputies, Nigel West Dickens and Seth Briars with the ultimate goal of assaulting Fort Mercer, the Williamson gang's hideout.