The Doctor couldn't help but actually cringe when the Master railed back at him, and was so full of self loathing that the only thing he could say in his defense to get the Master to stop was to curl his lips in an angry snarl and shout, "SHUT UP!"
In the short, silent moments that followed, the Doctor kept his gaze focused straight ahead, burning with hatred, not at the Master, but his own existence. "How was I to know it wasn't your fault?" was his last ditch effort to try and find some meager excuse for his behavior. "The only things I had to go on were your constant threats to Earth, my Companions, and myself," but it was said so miserably, that there wasn't any bite to his words.
Unable to keep eye contact with the other Time Lord, the Doctor idly picked at the loose fringe on the edge of the blanket he was sitting on, and muttered "Don't say I never needed you. This is me being honest, by the way, in case you can't tell. I... thought..." but then he gave up in mid-sentence, "... I don't know what I thought." He covered his face with his hand in shame, but tried with great difficulty to begin again. "When I begged you to regenerate, I thought I could help you. Heal you. Not just because you were the only other Time Lord, but because you were my friend."