AKA: So It's About Rhode Island, Right?
At what point did The X-Files lose control of its storyline. Arguably it never had control, it is very clear in retrospect that the plan for the story was functionally nonexistent and they had been winging it long before everyone figured out they were. But that doesn't need to be a problem, lots of decent stories weren't written with a game plan in mind, and they can work out. No, I think that the problem is a lot stranger and more interesting than a simple lack of a long term plan.