The Doctor sighed heavily as he punched in the coordinates for Leadworth. However much he didn't want to, it was time to let go of his sweet little Amelia. She had her own life to lead, a safer one than what he could offer. In any case, she was married. Why would she and Rory want to keep traveling with him when they could have a family? And hadn't he already gotten their first child kidnapped? They would never get those years back. Hanging around him was dangerous – he only left death and destruction in his wake.
Who was he kidding, though? The real reason he was so distraught over leaving Amy behind (yet again) was that he loved her. And it killed him to see her and Rory together, knowing that she'd chosen another over him. That's why he was taking them home – to avoid the twisting of the twin knives in his hearts every time he saw them kiss or hold hands or be anywhere near each other. Some Time Lord he made – over nine hundred years old and unable to handle seeing his two best friends in a relationship. Since when had his life begun to resemble one of those human soap operas?
Sighing heavily again, he brought the TARDIS to a halt. Hopefully he'd gotten time and place right. But, if he hadn't, it wouldn't be the first time he'd screwed something up. He'd made so many mistakes when it came to Amy, after all.
"Pond One! Pond Two!" he yelled, shaking his head to rid himself of such melancholy thoughts. What's done is done, as he often reminded himself.
"Eh, what's up, Doc?" asked Amy, coming into view hand-in-hand with Rory.
The Doctor forced himself to meet their eyes and not merely stare at their hands. Couldn't have them thinking he was jealous, now could he?
"I have something I want to show you," he said mysteriously, as was his way. "Come along, Ponds." Turning his back on them, he made his way to the TARDIS's doors, pushing them open without preamble.
What lay before them was a neat little cottage, similar to where they had been living in the dream world. A car was parked outside, all shiny and brand new. Amy and Rory stared from it to the Doctor to each other and back again. This went on for several minutes, while all was completely silent.
"Doctor …" Amy whispered at last. "Is this for us?"
"All for you, my glorious Ponds," the Doctor declared, beaming at them.
"It's too much," said Amy. "How could we ever repay you?"
"Amelia, I don't expect payment when I do something nice for two people I happen to consider my friends. And I certainly don't expect anything from you, not after all that I've already taken."
"Where would we have lived otherwise, Amy?" asked Rory, piping up, effectively ignoring the Doctor's self-deprecating statement, "In your parents' house?"
"That would be preferable to accepting his charity," she huffed.
"Is that what you think this is – charity?" The Doctor was stunned, "Oh, no – Amy." He moved to embrace her. "That's not it at all. I did this because I wanted to, because I felt that I had something to make up for, and this was all I could think of to even begin to atone for the mistakes I've made when it's come to you."
Amy wrapped her arms around the Doctor, holding on for all she was worth. She didn't really object to what he'd done. Her only problem was that she knew what this represented – the Doctor's parting gift, meaning that he was leaving them behind … again. So she'd chosen to lash out at the nearest available target – his generosity.
Pulling away, but just barely, she turned to Rory. "Could you give us two minutes?" she pleaded with him. If the Doctor really were to go away again, then she wanted their farewell to be private, just between them – the way it had been when she was seven, and the way it had been when he'd come back on the night before her wedding.
"Sure," Rory nodded, having also sensed what was going on. "I'll be seeing you, Doctor," he said, holding out his hand for him to shake.
Releasing Amy slightly, the Doctor returned the gesture. "It's been a pleasure," he replied.
Rory nodded again, before turning and walking into the new cottage to get acquainted with it – or reacquainted, if it turned out to actually be the same cottage as the one from their psychic dream.
The Doctor drew Amy back into the shelter of his arms. Keeping her head buried in his chest, she spoke, voice muffled slightly by the fabric of his jacket, "You're leaving, aren't you?"
"You haven't seen the last of me," he told her, though he had no idea whether there was truth to his words or not. He never knew. "Bad penny is my middle name," he went on, in an attempt to lighten the mood. "Seriously, you should see the looks I get when filling out a form …"
"Why now?" Amy asked, eyes brimming with tears that nearly made him come undone and give him cause to rethink what he was doing.
"Because you're still … breathing," he said at last, having been observing her carefully as he sought for the right words to use. And what he spoke was the absolute truth. As long as she was alive, he could go on. If ever she were to die, then his world would come to an end.
"You can't just drop me off at my house and say goodbye like we shared a cab, Doctor," she protested. "Not after everything we've been through – everything."
And how well did the Doctor know. But there was nothing to be done. There never was and never would be an easy way of saying goodbye to the people who meant the most to him. "And what's the alternative?" he asked her sadly, "Me standing over your grave? Over your broken body? Over Rory's body?"
Amy's response was instantaneous as she put her arms back around him and drew him near. Burying his face in the crook of her neck, the Doctor allowed himself to release the slightest of whimpers at the thought that this might be the last time either one got to hold the other.
"Tell me one thing, though," Amy demanded as she pulled away. "All those times on our travels… did I just imagine the way you felt about me? Was it all in my head?"
"Oh, Amy," he breathed. Brushing her fiery locks away from her angelic face, he brought both of his hands up to cup her cheeks before pressing his lips to her forehead for what would be their last kiss. "My sweet little Amelia – after all we've been through, do you really have to ask?"
He pulled away, and they shared a sad smile. But no more words were said, for none were needed. Doctor and companion stood taking the other in – memorizing the way they looked, right in that very moment – and each trying not to cry. Finally, when the Doctor could bear no more, he turned to enter the TARDIS. Pausing in the doorway, he raised a hand in what seemed to be a futile gesture that was less than adequate at summing up their shared experiences.
Really, the Doctor thought, Amy does have a point. How can this be the end, after all we've seen and done?
No matter. His path was set and now he had to follow it. Closing the door after him – and not missing the symbolism that he was metaphorically shutting the door on his and Amy's time together – he darted towards the controls of the TARDIS, eager to leave as soon as possible before he was tempted to go back. Laying a hand on the TARDIS, he thought of how she had been his one true companion through it all. But it wasn't enough – it wasn't the same as when Amy was on board. Turning in a circle, he half-expected to see his mad impossible Pond running towards him, babbling on about some new discovery she had made, some new room that the TARDIS had shown her.
Accepting, though, that Amy wasn't there – and never would be again – the Doctor leaned heavily against the control panel and, putting his head in his hands, began to sob.