Disclaimer: I don't own Stargate: SG-1, I'm just playing in the world. I mean no offense to the cast and crew of the show. This is just how much I love them for all the entertainment they've given me.
When I'm writing any one particular fic, what I usually find is I will have particular themes running through my head as I write. Sometimes I work them out beforehand while I'm plotting the story, or it's comes to me as a desire to incorporate something into a section which then finds its way into other sections and chapters.