Well, for my own story arc, I took inspiration from the game story itself. When I first heard about the Foundry, there was talk of creating campaigns and I was definitely excited about adding my own part to the Star Trek Universe.
I originally wanted to concentrate on the Federation vs Romulan conflict. But because Romulans were level restricted at +16, I switched over to the Federation/Klingon conflict. I also didn't want to exclude the possibility of a Klingon campaign so while designing a Federation campaign, I also tried designing a Klingon missions that would work opposite the Federation ones (for example, the Klingons capture an outpost and the Federation mission would be to liberate said outpost)
I also wanted to level restrict my mission to lower level (especially for the Klingons to help smooth their leveling process) so I wrote in that the player's ship and crew are called in to reinforce strike forces on their respective sides to give the feeling that the player was playing a part of a small conflict in a much larger war.
So I had finally set up a backdrop, then I started working out the finer details of my story, which I suppose is the part you are most interested. I worked out a broad overall storyline from watching/reading various shows dealing with similar concepts searching for stories that I found interesting and hopefully other people would too. I also learned a lot from playing other people's missions I used to do quite a few reviews as well so I could learn new tricks from the Foundry as well as see what I liked from other people's missions.
Very interesting. I've wanted to do a few gamma quadrant missions since we could technically fudge gamma quadrant systems to an exit point on the Bajoran Wormhole,
As I got into it I started wondering about full scale concepts for mission categories like... Lt-Lt. Commander Hard mode missions, and broader story arcs which, as I've started working in the foundry knowing what it takes to build sets... spent about 2.5 hours building a single engine room for a single part of one a single story that I felt would be appropriate for a defiant class ship.
Anyways as far as story goes, I know for me, I get caught up in Nicholas Meyers portrayal of the Star Trek universe, which is a touch more political, and a touch more militaristic, then what TNG did, but closer to DS9.
I wanted to build missions and stories where, you're not exactly the central focus. You're not the hero, your part of an organization that, contextually with the 2409 story line is approaching its breaking point fighting so many wars at once.
I dunno, Star Trek and it's stories have always been very philosophical to me. The Enterprise, or DS9, or Voyager, aren't exploring the galaxy, but, instead the nature of the human soul which is why the major alpha quadrant powers behave more like archetypes from human history then really strange aliens that we need to understand.