It takes Johnny's confusion and hesitation for the TARDIS to realize that he hadn't recognized her, that perhaps he never really saw her humanoid form through the tears and the pain. "Yes," she confirms just as softly, then recalls the bits and pieces she'd been able to glean from his mind. "John. I am sorry for what happened to you. I had no intention to hurt you."

She doesn't understand why he's fine now any more than she knows why he reacted so catastrophically to her two weeks ago, but she's rather glad for it nonetheless. "Do you have any guess as to what about me caused you such pain?"