The Doctor hardly notices the other's sudden confusion, he figures he's talking for his own benefit anyways since the other had seemed a bit too anxious and hazy to want to listen. Still, he was hoping the other would at least absorb some of it. He didn't know what was going to happen here, but the feeling about this place, the darkness and misery just seemed to eminate from it's every surface.
"What I don't understand is that if you have that brillaint ability...why don't you just escape? They can't keep an eye on you all of the time. and at least out there you'd be free.", he sighs, hitting his head against the wall gently. "All these years running and I've never been caught. I think you're the first you know."
He looks to the other with a smile, finally noticing that he had the other's attention though he seemed a bit more than simply confused. "It's alright.", he tells the other softly, meeting his gaze. "Just breathe, okay? If you panic you might draw their attention." He motions to the men outside, flinching a little when he hears something crash against the TARDIS' doors.