The Doctor looked up from the TARDIS console at Amy and Rory, the latter of whom was standing in front of him with the determined ease that can only truly be pulled off by a man pretending not to be nervous about something his girlfriend has pushed him to do.
"Something's been bothering us."
The Doctor frowned, stepping away from the console and looking from one to the other of them and back again.
"Oh. That's not good – yesterday you wouldn't have noticed anything but each other unless it fell between you from the ceiling and then you only would have glanced at it, so if something's bothering you you've either had a fight or something is extremely wrong, and if you're saying 'us' and Amy's standing there laughing at you trying to follow what I'm saying I'm guessing you haven't had a fight. Not that I'm saying I wish you had. What is it?"
Rory took a few more seconds to process this than the Doctor's approximate three to say it, and Amy's suppressed giggling behind him wasn't helping him think.
"Uh – well... Remember when we were in the dream world?"
"Ah, the angry pensioners. Yes." The Doctor leaned back against the console with an almost nostalgic look on his face. "I wish I could say 'good times,' but... no. What about it?"
"Something you said. We've just now realized it, and... well..." Rory broke off, not-quite-wringing his hands and almost-turning to Amy in an aborted near-plea for backup, before quite-definitely-bouncing on his heels and snapping back to face the Doctor.
The Doctor flicked his eyes sideways as if in thought, sticking his hands in his pockets and leaning further back, speaking at first in an explosive exhale. "Ohhhhh, something I said... That leaves a rather large array of possibilities to sift through."
"When we were talking to the Dream Lord," Amy cut in, finally coming to Rory's rescue.
"Ah. That narrows it down a bit."
"You said you knew who he was because there was no one else who hated you as much as he did."
He shifted slightly, taking on the expression of one who has grasped the point of the matter but isn't about to admit it.
"That I did, yes."
Amy folded her arms and gave him an 'I-know-the-game-you're-playing' stare. "You told us the Dream Lord was part of you."
"Yes," he said easily, as though owning up to a comment made about the weather, and left the rest to the two of them.
Rory took his turn to speak. "You can't... I mean, do you really hate yourself?"
The Doctor shrugged, pushing away from the console and pacing calmly around it to fiddle with a few controls on the other side. "Bits of me hate other bits of me, yes."
"What does that mean?"
"It means," said the Doctor, turning a crank that had shifted a few ticks to the right since last anyone had taken notice of it and looking up at them with a smile that was more subdued than either was used to but more genuine than the moment seemed to call for, "that I'm not the same man I was a hundred years ago, or two hundred, or three. And that I've done things I'm not proud of. Things I'm not sure I've forgiven myself for."
Rory started around the console to where he was standing and found that it was suddenly where he had been standing as he deliberately not-deliberately took a few steps away, flicking a switch he had apparently just spotted. Rory didn't close the last bit of distance, but he stared hard at the Doctor and asked – didn't demand –, "Like what?"
The Doctor stopped moving for half a second. Then he looked up at Rory and there was no trace of a smile left on his face. "Things I certainly wouldn't expect the two of you or anyone else to forgive me for."
While Rory tried to think of something – anything – to say next, Amy stepped around the console on his other side. She moved between them and laid a hand briefly on the Doctor's arm, saving them all from an awkward silence by saying quietly, "So don't tell us. Because we both think you're... amazing, and I know it would take more than a few skeletons in your closet to change that, but if you think otherwise, there's no need for us to know anything." While the Doctor fumbled for some sort of response to that, Amy gave Rory a pointed look and, when he failed to take her meaning, elbowed him in the side.
He managed to turn his yelp into a "What? Oh. Um, yeah. Yes, definitely, what – what she said. You're amazing. And I wouldn't say that to any other bloke who'd kissed my fiance, so – so I don't know what else you've done that you think would make us – me, at least – hate you. But you don't have to tell us."
The Doctor cleared his throat and stared intently down at the console for a few seconds, pulling and pushing aimlessly at various controls.
When he looked up, his eyes were bright and he was smiling – not the manic or laughing or exhilarated grin they were used to, but a small, closed smile that somehow left him looking the most honestly happy either of them had seen him yet.
"Amazing?" He flicked his eyes between the two of them, expression never once wavering. "Skeletons in my closet, Amy? I've got a whole basement's worth I could show you. Rory, pointing out first of all that Amy kissed me, I could tell you stories that would have you trying to push me out into open space, and Amy, if you heard, you'd help him. Amazing? I could give you a hundred reasons why you're wrong about that without even thinking, but do you know what?"
His smile widened. "Rory Williams, Amy Pond..." He clapped a hand on Rory's shoulder and drew Amy into a one-armed half-hug. "For the moment – for a little while – I think I'm just going to let myself believe you."