Author's Note: Written rather quickly tonight after a Series 5 finale rewatch, so excuse the quality (or lack thereof).
The shaking and roaring of the TARDIS gradually subsides as she slips into the time vortex. After a few moments, they're able to stand upright without clinging to the console for balance. The Doctor slaps down a final lever with a flourish and claps his hands, spinning around.
"Right, then." He beams at Amy and Rory, still decked out in their wedding finery. "You'll want to go change into something warmer, we're heading for winter on Thelm."
Amy frowns as she begins removing her bridal veil. "I thought we were going to the Orient Express."
"In space!" the Doctor reminds her gleefully. "Specifically in a very shabbily-researched Thelmian museum of old-Earth history, a sort of historical anachronism enthusiast sort of thing. They've got it all in the wrong order of course but it's still brilliant. I know their head archivist. Lovely girl, four arms, very good dancer." He stops pacing and stares at both of them. "Are you still here?"
Rory glances around them and then nods hesitantly.
"Clothes! Warm! Go! Get!" He grabs both of them by the shoulders and steers them towards the nearest corridor. "And grab my usual set while you're in the wardrobe, will you?" he calls at their departing backs. "You might have to dig for the bowtie, I was in a hurry before..."
He watches them leave, and then collapses into one of the chairs by the time rotor. His eyes flutter shut. "Too much dancing," he murmurs to himself. "Don't dance so much next time…"
He doesn't realize he's fallen asleep until Amy's voice wakes him. "You okay?"
The Doctor's head snaps up. "Yes! Sorry. What?"
Amy is smirking. She's on the other side of the room, dressed the way he's used to seeing her again, hair free of flowers or combs or veils, familiar red scarf slung around her neck. He finds himself smiling at her, his heart swelling unexpectedly with deep affection, until his gaze drifts down her arm and stops at the wedding ring glinting on her left hand. He swallows and clears his throat.
"So, has Rory gotten himself lost in the shoe section again?" he says in an attempt at casual.
Amy raises an eyebrow. "Who?"
He stares at her in horror.
"Oh my god, I'm kidding," she sighs, walking over.
"You've evil," he mumbles, and suddenly she's sitting down on his lap and putting her arms around his neck. "Oh. Hi."
"Hi," she whispers into his hair.
The Doctor's arms migrate up around Amy's back, and they hold each other for a few minutes, saying nothing. The weight of her across his legs, her arms curled around him, one hand on the back of his head, the other resting between his shoulderblades, the smell of leather and perfume and her hair—he realizes he's blinking rapidly, tightening his embrace. His best friend. Oh, how close they came to never seeing each other again.
He hears Amy sniff and draws back a little. "You're crying," he states, fully aware that his own voice has gone husky.
"Shut up," Amy mutters. "'Course I am. I missed you. I went my whole life missing you and I didn't even know it until today. Because you had to be brilliant, and clever, and save the world, and leave us all behind, and don't you ever do that again, Doctor, don't you ever make me say goodbye to you like that again…"
She's crying in earnest now, shaking the Doctor's body with her sobs. He weeps a little too, then, his tears leaving dark spots on the back of her jacket as she tries to talk. The words aren't important. He understands her anyway. He allows himself to kiss a strand of her hair and feels his heart constrict with tenderness. Nothing can be more important than this. She should be loved perfectly and wholly, this astonishing creature beating against his heart.
She will be, he thinks dully as she unwinds herself from him and sits back, by Rory.
He tries to take a deep breath and tell her something really bracing and cheerful, but he can't because suddenly her lips are on his. They persist for maybe a second or more, just long enough to set his pulse wild, and then they're gone, Amy moving back and clearing her throat awkwardly.
"You're married to Rory," he says in a low voice at the same time as Amy stammers, "Sorry."
"Yeah—I know, I wasn't—I just—" She brushes her hair away from her face, blushing faintly. "I didn't mean it like that. I'm just…thanks for coming back."
"I always come back," he says automatically, unable to take his eyes off of hers. "Amy—"
"Yeah, I know, shut up." She claps him on the shoulder and then slides off his lap, standing up and straightening her skirt, wiping the tears off her cheeks with the back of her other hand. "No more of that, I promise. Married now!" She gives a little gasp of delight and folds her hands together. "What if we have kids? Can you imagine, little kids runnin' all over the TARDIS? You could be their godfather! Well, god-alien. Uncle Doctor! Ha ha!"
She's long gone now, wandering in a circle around the console and rambling about babies and Rory and how weird it is that she actually knows what it feels like to be pregnant even though she's never been and how she's sort of always liked the name Gretchen but secretly hopes Rory will talk her out of it. The Doctor stays where she left him, hands at his side. He can't tell if she's talking to fill the silence or if she's genuinely excited. He doesn't know which he'd prefer.
He realizes that until this moment, he honestly thought he still had a chance.
Rory stumbles back into the room, dressed warmly and with the Doctor's outfit draped over his arm, and Amy kisses him brightly and asks him what took so long, and that's that. They turn together and look at the Doctor expectantly, and he knows it's time for him to leap out of the chair, snatch up his clothes enthusiastically, disappear behind a closed door for a few minutes, and then dash out and pilot the TARDIS to Thelm with one hand while fastening his bowtie with the other.
He takes a deep breath and tells them something bracing and cheerful, and then he does.