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Bad Wolf, is the writing on the wall. The Doctor hadn't been in the right position to read it before. It probably wouldn't have changed anything, even if he'd seen it earlier. Maybe just that his breath would've hitched. It doesn't now, his lungs filled with water as they are.
It hurts, to think of her seeing him like this. On some level, he'd known all along that she must have witnessed every second of what becomes of him without her. He couldn't have helped it.
He hopes that the words mean forgiveness. His eyes slip closed all too easily.