The Doctor doesn't know what to say for a moment, he does feel deeply touched and he sort of feels Rose taking his hand on Satelite Five when he mentioned his planet burned. Expect, he didn't tell her, that he was the one who did that.

He would love to come terms to with himself for what happened but he's a monster. The remark John makes The Doctor looks at him rather curiously.

He wants to be let free of his guilt and here someone is trying to reach out to him. The Doctor is breathing in slow and deep breaths because he wants to say something. To test this but he's afraid.

"I - I ended the war. I killed them all."