A/N: Having of course not seen Angles Take Manhattan, I don't know what fate causes Amy and Rory to leave the Doctor. But I do know that if his Amelia were to be tragically taken from him, the guilt would be unimaginable. I think she knew that, too. I couldn't even handle that scenario in my own head, so I wrote this.
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The Doctor felt an immense emptiness in both his hearts for Amy and Rory. They were more than companions or even lovers; they had been family to him. Which was something he had not experienced in such a long time.
And...he'd lost them, too. It was his fault just like always.
"Doctor," said a very familiar yet impossible voice. Amy Pond. Well, technically a hologram of Amy Pond, standing not far away in the TARDIS. "I'm recording this in case, um, something happens to me. There are things you should know, and if I get left behind or have to stop travelin' with you for reasons beyond my control, I hope you'll see this. I'm preparing for the worst."
"So Scottish," he laughed softly.
"Because the last thing I want, Doctor, is for you to blame yourself. If I...died somehow, it wasn't your fault. Please believe that for once. I can't handle being another thing you feel guilty about. Look at me, I'm crying over something that might never happen. Doctor, you're my best friend. You didn't ruin my childhood or my life and I've never, for one second, regretted meeting you.
"If it weren't for you, I'd still be alone in that too big house with Prisoner Zero hiding in it. My life wouldn't ever make sense, or maybe the crack in my wall would erase me, too. I'd never have eaten fish custard or seen the universe. River would be a completely different person without you, and we both know she'd hate that idea. She loves you so much, Doctor. We all do."
"Oh, but Amelia, if it weren't for me you could have a normal, safe, happy life with Rory and raise your baby. You would still be alive right now."
She couldn't hear him, of course.
"What I'm tryin' to say is, no matter how it ended, I wouldn't have missed this for the world. And hey, it really was the best, yeah? Don't be alone forever. Please do that for me, Raggedy Man, as well as for you. Be good to my daughter. Tell Rory I love him if you can. Of course he already knows. Have amazing adventures. Try to save the world in fifteen minutes, that sort of thing." She turned her head to look at him, her holographic face streaked with tears.
This was the last word of Amy Pond before the image vanished: "Gotcha."