I talk the ideas through, to myself. For example, my current game starts with the protagonist being exiled from home. He wants so badly to go home --- but has no idea where that is...
He crashed to the town in, well, a meteor (although the characters don't know that, I make it blindingly obvious with an impact crater and about half of the starting town severely damaged). His true home is a different plane of existence. So, I do something like:
"How would he get home?"
"Well, he can't get to another plane by himself. At least, not yet. He needs help."
"Help might come from the incarnations of various elemental forces. Said incarnations would help him."
"Why?"
"Because they've been forced to by the protagonist's father."
"So, is the protagonist good or evil?"
"I think it would be more fun to have the game be all about shades of grey. Good noble people doing horrible things, and horrible acts sometimes having great outcomes. Just like real life."
So I basically bounce ideas back and forth. Often, I find what seems a good idea completely changes when I go to implement it in the game. At first, there would be 3 Knight types the player can become (White, Grey and Black) through a specific choice. Now, I've decided instead the player can choose to join various Guilds and change class, such as from a Knight to an Assassin. And he can be Blessed even as an Assassin, giving him new skills...
All of those flow nicely into my original idea of shades of grey. Why can't an Assassin be Blessed if he partially atones? And who says a Knight's typical tasks are always Good? Even a just ruler must make hard decisions.
I rambled on quite a bit there, but that's basically how my thought process goes.