The best way to plan a DF scenario isn't so much to have a plotline in mind so much as to flesh out your antagonists, their motivations, and their resources, and just work logically from there. That way, they can act and react to the PCs in a natural way.
Basically, play the antagonists like PCs--they have a goal, and you walk through their efforts to reach that goal.
Also, never, ever be afraid to modify your plot if your players come up with something good you didn't think of. They have a part in creating the story as much as you do, after all, and that includes occasionally modifying a villain's plan because the PC came to a logical conclusion. Players should always be rewarded for creativity, initiative, and figuring stuff out on their own.