I wonder what the doctor might have seen in room 11 (11 for 11 regenerations?). I'd suspect that the thing he might be most scared of is himself. After all, he has been responsible for a couple of effective genocides (or more), and he realises in this episode how dangerous he is to his companions - a theme which Rory amplifies too.
Yup, I figured it was himself. "Of course. Who else would it be?" Not "what". Definitely himself.