In contrast with The Faction Paradox Protocols, which was comprised of three two-part stories, Alan Stevens described The True History of Faction Paradox as "a six-part story".[2]
The series was produced by Alistair Lock, who had just produced Kaldor City for Magic Bullet Productions, rather than The Faction Paradox Protocols producer Nigel Fairs, who had already begun producing Sapphire and Steel for Big Finish Productions with many of the same cast members from Protocols. To avoid having to recast too many characters, Stevens asked Miles to minimise returning characters; while Justine, Eliza, and Lolita were essential to the ongoing story, Lord Sandwich and the Sieur d'Eon were left out.[2]