On occasion, I find that disparate elements in a sandbox game come together seemingly of their own volition. Stories and plots rise organically out of a motivated, involved party.
This is why I love my SWN game. Though I only have two players, they take things in directions I don't expect, and this leads to greater things than I have previously thought of.
I like leaving parts of the map blank, literally and conceptually, so this kind of thing can happen.
(Yes, guys, if you are reading this, I am intentionally being vague. I wouldn't want to spoil the surprise for next time, right?)
I've also decided to take a page from DCC for this SWN game. Having grown very attached to an ordinary hireling, the PCs wanted to know what they had to do to promote her to a 1st level character. They already pointed out that she's survived captivity by space pirates and other perilous events. I decided that she, being effectively a zero level character, needed to survive an adventure. Turns out that surviving a dog fight with an alien spacecraft that blows your ship halfway to hell counts as surviving an adventure.
I embrace the idea that PCs and NPCs don't play by the same rules. I think this Right and Proper. Trying to fit everyone into the same mold leaves us with absurd crap like 12th level commoners in 3.x. That, however, is another post for another time.