just another thought, thinking Kirk style at least, what if after their nebula is lost, they tell star fleet whats happening, since sect 31 is behind it, they order you and your crew to forget what happened over there, thus you and some of your crew steal a ship, and why not one of the most powerful ships in the fleet, maybe a couple ships since we have fleet commands now, and go and expose whats happen, star fleet under sect 31s pressure sends a small task force to stop you, maybe battle with DS9 ensues, and somehow you convince them of whats happening, you take the task force that attacked you along with your rag tag fleet and go and expose sect 31 and stabilize the Gamma quadrant, and you and your men come back a hero
just some ideas, since I read this thread earlier, random ideas keep flying around me head. I tried balancing, story, twist, battles, and negotating