In July 2015, they announced that the game would be broken up into the two episodes, known as Side: Above and Side: Below, as they thought the story had gotten too long to be sold for 15, with Side: Above being roughly the same length as Fault Milestone One, and they wanted to avoid raising the price to match. Due to this split, they had to rein in some story elements, which Munisix later stated was a beneficial thing, as those elements could have otherwise gone out of control. Munisix briefly considered giving Side: Below the title of Milestone Three, but decided against it as they wanted each "milestone" to have its own consistent theme. For Fault Milestone Two, the theme is explored in different ways in each of the episodes. They were designed so that they could fit around the upcoming prequel game, Fault: Silence the Pedant. Like with Fault Milestone One, the developers wanted to include one player choice in Side: Above; they had one in mind, but eventually had to remove it as it broke the flow of the story. A new presentation system was added for the game, intended to make the experience more immersive and feel "larger than life".
