The Doctor sometimes forgets just how powerful his stare can be. Might have something to do with the fact that it doesn't work on Clara these days. When he sees KITT move suddenly and the black streak he backs up a step himself holds his arms up and then slowly kneels. Not so much an act of vulnerability as it is to show that he respects that KITT could easily kill him.

"I haven't been in this place long. I'm worried about the TARDIS. Everything is suspect."

That's about as close to 'I'm sorry' as the Doctor gets these days. He's obviously more worried about her than he is for himself.

"If you are as connected as you say, I would greatly appreciate your help. Is she doing all right... with the energy in this Universe. Is it harming her?"