Maybe this is a silly suggestion, but why not just use "your" story as the plot? Just re-flavored to something that works for the themes you like. So instead of you being unable to make a story plot, maybe you have something like how the farming villagers that live in a medieval kingdom cannot make their "plot" of land produce -- and so, your kingdom can't seem to get farming, trade, or other forms of commerce going -- so your story could maybe be for the people to figure out why they can't get things to grow. Maybe the land is cursed, and you could find this out from puzzle solving or exploration? Maybe there are monsters that regularly ruin the land. Maybe the place is war-torn, and the fields are barren because previous wars burned and salted the earth. I think what your story specifically is should pair with the kind of mechanics you want to include, as certain types of stories probably lend better to some things more than others.
You can then use the things that you struggle with as actual story ideas. "I can't think of any bad guys" -- great, your bad guy steals peoples' memory or creativity in some way. Perhaps in your story there's some sort of dark magic, seeking to consume parts of the world, and they need to be beaten in order to keep the world whole (you know, your "plot holes" tearing apart your story's reality...)
Maybe these ideas can spark something for you?