The Doctor really didn't seem to want to put the pieces together. He'd been piecing up enough lately trying to figure out puzzles and games laid out by the man behind the curtain. The Doctor never thought he might actually want to see the Cybermen - but, at least he knew what sort of danger to expect from them and how to defeat them. Or, maybe the Sontarans, they were easy enough to manage.
"I suppose the term alien is technically correct, though in my mind you lot are the aliens," it was a matter of perspective, really. "Oh yes, quite human looking. Though, I could say you all look like natives of Gallifrey."
The Doctor was drumming his fingertips on the floor beside him. As he thought a moment. "I suppose it's only fair we keep our secrets to ourselves, yes? I've had enough people react badly to the Time Lord in their midst that i'd rather not experience it while enclosed in a big glass box."