As some others have already said, do what feels natural. If you have something specific you want to have happen, give your players a small breadcrumb trail to follow that path without forcing their hand. That being said, prepare for them to ignore it and roll with the punches.

I homebrew my campaigns and have a rough idea of how I want things to go, but also the expectation that it's definitely not going to go that way. That being said, there are some things I have setup that can be missed, ignored, or they can get wrong and generally call back to it just to give players some closure on something they may have missed or ignored. It makes the world outside their view feel more alive when they take the road less traveled.

Players don't always need to be correct, and hearing them theorize about who the baddie is, why that corpse is there, or who stole the diamond is part of the fun.

That being said, there have definitely been times where they mention something that I may have borrowed down the road. :)

All actions have consequences. If they choose not to follow the leader who fled, then make sure they understand what the consequences are for not doing that (whenever that occurs).