She'd only started sleeping in his room after Rory died. The first night he had been reading in his room, long after he thought she'd gone to bed. She'd quietly knocked on the door, and asked to come in. He opened it to find her there, her fiery hair pulled messily into a bun, and her eyes red. He didn't ask her any questions, just held the door open and watched her settle herself in the bed. There were no words exchanged that night. He had just held her as she cried, with the pain of losing something she couldn't even understand she had lost. He'd assumed that it was a one-time thing, that the first night would be the hardest. But as each successive night, the tentative knock came on the door, he'd leap up and let her in. It didn't seem to matter what kind of day they'd had, what sort of adventures they'd run across, each night the pain of not-remembering seemed to come flooding back to her.
"Sometimes I catch myself trying to remember something." She said one night, legs flung across his as she sprawled across the bed, she was painting her nails. It must be a good night, he thought, she wasn't crying, and she was talking. She hadn't talked about it once in the weeks that had passed since Rory had vanished. "It's weird, I can remember everything. I've always had a good memory. I can remember everything, but it just seems like something's missing." She sighed, paused, the brush held mid air above her hand. "I don't understand. I wake up, and it's like seeing something out of the corner of your eye. I've almost remembered what's missing, but then I wake up properly and it's gone."
"I know how you feel." He said, patting her ankles. "I've lost enough people that it always seems that there's that little ache in your heart."
"It doesn't feel little." She blinked back tears and determinedly applied the polish to her nail. "I don't know. It must be nothing. Maybe I'm just not cut out for this life."
He pulled her up to him, spilling the pot of brightly coloured polish on the bedcovers. He held her face in his hands and said sternly, "Amelia Jessica Pond, the very fact that you care so deeply is exactly why you are cut out for this life. I'm very very old, and because I am so very very old, I am always in danger of not caring. Of not seeing the wonder, beauty, and yes even pain in this vast universe." He pulled her into a tight hug. "Without you, I would be lost. I couldn't do this without someone to help me. And you Pond are a one in a trillion. And if there's anyone who could say that with authority it's me." She half-laughed half-sobbed, and clutched at him more tightly.
He felt guilty most nights because he was glad to have Amy by his side. The rise and fall of her breaths, the warmth of her sleeping form, it comforted him. It lifted some of the burden from his shoulders. He remembered Rory, how could he ever forget wonderful, brilliant, brave Rory, but Amy didn't even have that to comfort her. She just had him, a stupid 907 year old alien, who couldn't even save Rory. He remembered her words, 'What's the point of you?' What was the point of him, if he couldn't even save the people he loved. So these days he took comfort from the presence of Amy beside him, always. He didn't care that it was supposed to be Rory lying here next to her, he didn't care that she spent most nights crying on his shoulder for a loss she couldn't remember, he had her next to him, and that was all that mattered.