Going through the mission scripts, I found something so weird and bad that I can’t believe it hasn’t been noticed before. Apparently at some point in time I decided that faction missions shouldn’t scale by the PC’s renown; instead, each faction has an independent difficulty counter that increases each time the faction loads a new story. This is not necessarily a bad idea. What is a bad idea is that the difficulty counter is raised by 16-25 renown points every time the story changes. At that rate, the faction mission difficulty level could potentially reach 70 in the first week of the game.
As near as I can tell this system was introduced around release 0.600 and abandoned shortly thereafter. However, I didn’t bother to refactor all of the missions that use it. So now it is randomly scattered throughout the series folder.
This is going to be more fun than a locked room full of monkeys.