The thing about the Doctor was, you couldn't trust him.
Sure, he gave you that line—Trust me, I'm the Doctor—with that mischievous grin and you wanted to trust him, you wanted it to feel like when you were a kid and you believed in faerie rings in the forest and the monster in the closet and that your body would always feel so invincible and you wouldn't get older and age and fall apart. But after an almost-death at Lake Silencio and another almost-death in Berlin and the way time broke apart and River re-broke it and set it somehow right again, Amy wasn't sure if she could ever really trust the Doctor again.
Something about being back in the Tardis felt different now. After the Doctor had come for Christmas, he left again until after Easter, which is when Amy and Rory were invited back. Looking back, Amy remembered the old adventures with great fondness, but with a shocking realization that she—or Rory—could very well have died at any time (a real death, not just a time-forgiving death like Rory had done). It all seemed so reckless, but here they were again with the madman in the box. Now, Amy realized she felt slightly wary about where the Doctor may be taking them. She wasn't sure they'd make it back all right this time, and Amy, sitting alone on the steps in the control room of the Tardis, wondered just how much time she had left.
"Ruminating, Pond?" The Doctor whispered in her ear, making her jump.
"And where have you been?" Amy replied, half-attempting to change the subject.
"Not sure," thought the Doctor out loud. "I was trying to retrieve a loom room from a previous incarnation but I got a bit…turned around…" He trailed off, lost in thought.
"A loom room?" Amy snorted.
"Yes! It's a room…with looms! Really, Pond. Oh, by the way, Rory's reorganizing the books in the library. Something about 'alphabetical order', which to me seems totally ridiculous…" He muttered to himself as he twisted a few knobs on the Tardis' main console and checked a screen.
"Doctor?"
"Yes, Pond?"
"If anything ever happened to Rory and I, what would you do? Would you, like, go back and visit us? Would now-Doctor go back and pretend to be then-Doctor and take then-Rory-and-Amy on new adventures?" The Doctor whirled around and leaned against the console, an eyebrow raised.
"Amy, you're not making any sense." He crossed his arms across his chest. Amy paused, thinking how to phrase what she was going to say next.
"I just want to know that if something happens to us now, you'll be there—more—in the past. Do you know what I'm saying?" Something in the Doctor's face changed. It softened, became sad and infinite. He walked over to the steps and sat next to Amy. He sighed.
"I don't like to look backwards," he said softly. "It's always onwards and upwards, but you know that when you're ready to stay behind (because nothing bad is going to happen to you, Pond), I'll always remember you—and Rory—fondly. You're like my family. Besides, you've already lived back then, haven't you? You know I don't show up at any time." She looked at him and smiled sadly.
"Yes, but…" Amy paused, and collected her thoughts. "Memories aren't recycled like atoms and particles in quantum physics, Doctor. They can be lost forever, or replaced, or…" The Doctor looked into Amy's eyes, and in his eyes, she saw the infinite galaxies he'd traveled.
"Time isn't kind or unkind, Amy," the Doctor said matter-of-factly. "Time is unbiased. It keeps going and it doesn't care how we react to it. You might think I'm powerful, or wise, but if you really look at it, I'm at the mercy of time. I have to do as much good as I can with the time I'm given. And I have to keep you safe, which isn't always easy, given your fondness for wandering off." Amy made a face.
"I guess I just can't imagine a day when you're not going to be a part of my life," she said quietly.
"Me either," he replied, so softly Amy almost couldn't hear it. They sat in silence for a moment.
"Well!" The Doctor sniffed. "Aren't we a pair of downers? And us on our way to the Purple Forests of Ithra! Come on, Pond." The Doctor stood up, stretching his long arms. "Let's go see what that husband of yours is up to—I really hope he's managed to steer clear of the swimming pool." As if on cue, a cry of "Whoa!" came from the library, followed by a great splash. The Doctor groaned and rolled his eyes and started farther into the Tardis, towards the library. After a few steps, he turned around.
"Everything's going to be okay, Amelia. Don't worry. I won't forget you if you don't forget me." She half-turned back to him, her face partially hidden by a curtain of flame-red hair. He could see her smile and turned on his heel, leaving the control room.
What he couldn't see was the single, small tear rolling down her cheek.