It's not the appearance of the other so much as the sound that makes the doctor nearly jump out of his skin, especially after sitting in the dark for so long. The hiss is enough of a warning for the Time Lord, but his body won't cooperate of course, not yet. He's never considered to be that much of a threat, but the man's outright hostility, the sharp hiss and the sight of those hard yellow eyes easily tell the Doctor that anything he asks most likely won't be answered.
He opens his mouth as if to speak before suddenly darting in the other direction, his pulse pounding in his ears. He needs to get away and try to think this whole situation over. For him fighting is an option, not when he can just barely sense something here is off.