
I'm working on a story that's a prequel, and am having trouble coming up with an overarching plot, even though I think the setting and world problems of that part of canon are interesting and unique. I want to design out almost entirely the part of the story that takes place and that the canon actually covers, but it's still giving me what I call "Caprica problems." Which are,
1. The earlier events aren't as dramatic or ultimately important as the ones covered in the canon proper. In the case of the BSG--although I'm not writing BSG--mythos, the First Cylon War and surrounding events aren't as dramatic as the fleet or survivors, and in any case, we know any successes are going to prove empty, because we know it's not really over and the war not really won.
Knowing what comes later drains the sense of stakes.
2. Kind of picks up from part of one--the canon set for earlier events are designed to serve the story canon is actually telling, not their own. So the highs and lows are already set-up to not compete with the drama of the proper story, and the events and world building may not hang together for their own sake. You didn't need a cohesive history, for example, for Admiral Adama. You just needed enough to make Apollo feel overshadowed and tortured by duty, and enough to give the world a sense of history. The bits you see might not have a good arc once you start stringing them together, and might not be easy to build on, but either way you're constrained by the precedent.
3. The story has already been told in asides, flashbacks, character conversations, and via the canon proper--we know how the long game ends. Any important questions have already been answered by virtue of us knowing the outcome of the story that happens later.
You have to come up with new, entirely different questions to ask. Otherwise its just filling in spaces that most of the time were intentional "negative space" (story wise) anyway. That is, "seduced by the dark side" is scary and romantic when that suggestion is all you know. The play-by-play just kills the mystery.
Anyway. All of these are kicking my ass. Plus the canon for the prequel events contradicts itself pretty blatantly in parts, so that's a help, show. It really is.