For setting up the universe & situations, I'm pretty much in control -- subject to considerations of plausibility, etc. But once I get the ball rolling, the characters can start to get uppity
Fifteen years ago I wrote a Blake's 7 fic and created a minor character - an underling - just so the bad gal would have someone to talk to & beat up on. I was quite surprised when he informed me that he'd had enough and was going to stage a coup d'etat. It worked out well for my storyline, though. Lois has done much the same to me, too. But in my experience, when I followed their lead I got a more interesting story out of it.
It's like real life, I think. God sets things up and arranges circumstances, but we all have free will, and so the story wanders from the original intention.
A major difference, of course, is that our fanfic worlds are all self-contained (mostly). If Yvonne cuts of Clark's leg or someone kills Lois, it's not going to affect my story. Real life is much messier.
PJ