Just as a side note: does it bother anyone else that Rory and Amy haven't said a word about Melody since Let's Kill Hitler? Even knowing that she'll live to adulthood, I can't help but think they'd be a bit more concerned. Thus I'm forced to assume that we're not seeing everything, since Doctor Who is usually better about things like this than that.
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It's Rory snapping angrily at him about not checking up on the planets they visit before making touchdown. Talking about checking history books for plagues and how irresponsible he is and how he plays fast and loose with the lives of his companions.
No, wait. It's Amy staring at him across a room, except it's not Amy, but an Amy who should never have existed, fifty-eight years old in less than a day and so, so broken. The girl who waited too long, the one the Doctor finally had to shut the door on. The Amy he abandoned for good.
Then again, the Doctor can think of a host of others it might be.
Jack, whom he leaves in the lurch every time, whom helped to curse to immortality, Jack who just can't catch a break.
Martha, walking the earth for a year. Martha, whom the Doctor could never see because he was too hung up on Rose to ever notice anyone else.
Rose herself, trapped in a parallel universe, coming so far to find him, and in the end, he couldn't even tell her he loved her.
River, whose life he ruined long before he ever met her. River, who even when she was mad as a hatter still seemed to love him, and he couldn't do anything but look at her, every time, and see a stranger.
Donna, sobbing in fear, begging him not to make her forget. Donna, who would have rather died with all her wondrous memories than live for decades more without them, never knowing just how significant she'd been.
And a thousand more. Honestly, the Doctor can't sort them out anymore. There's just too many faces for him to search through, thinking of all the ways he's hurt them. If he ever devoted any serious thought to it the act of thinking of them all would take days, if not weeks.
"Where is she?" Amy's voice, still slurred and groggy with sleep and the after-effects of anesthesia, barely reaches the Doctor's ears, but it rings loud and clear in his mind, all the same. He's moved out of sight, where Amy's eyes can't find him, and left Rory to deal with the fall-out.
Fiddling with various controls on the TARDIS, trying not to think too hard on any one thing, the Doctor also finds himself trying not to listen, but picking up snatches of their conversation anyway. Rory's voice has a barely audible but instantly noticeable tremor; he stumbles over his words at points. ("She stayed"… "Said not to"… "Doctor"… "the door"… "the Doctor said"). There's enough shame there to fill an ocean, even if Rory's tones barely rise over a whisper.
"What do you mean the Doctor left her?" Where Rory seems saturated with shame, there is absolutely no mistaking the indignation in Amy's voice. "What do you mean the two of you just left her there?" Though she is still too sedated to properly express anger, her voice rises over the background noise of the TARDIS and the Doctor is glad, honestly glad that she can't see him and he can't see her. He doesn't like to think of the expression that must be lurking in those piercing green eyes.
Eventually, all falls silent. Amy, with the Doctor's heavy felt coat draped over her, falls asleep again and Rory, rather than going back to a more comfortable bed, settles down beside her, his arms wrapped around her shoulders and nose buried in her long hair. The Doctor is careful not to make any loud noises as he goes about the business of keeping the TARDIS going, for two reasons. One, he wouldn't want to wake the two lovebirds up—Ahh, look at 'em. Two, he still doesn't want to wake them up, but for a far less charitable reason.
What can he possibly say to them? To either of them?
"I don't want to travel with you!"
It takes a great deal, the Doctor has come to learn, to make Rory break down and shout. He's normally so calm and, if not collected than at least he doesn't scream and run away at the slightest sign of danger or hardship. Rory stands his ground where lesser men would balk, retreat. He keeps his cool under emotional strain as best he can.
Of course, if Rory doesn't shout easily, he also has never been particularly shy about letting the Doctor know when he thought he was being irresponsible. The Doctor is very careful about choosing his companions and he doesn't mind having one around who's willing to keep him in check—someone has to puncture that raging ego every once in a while—but Rory has had, from the beginning, the annoying and uncomfortable habit of hitting the nail right on the head when he calls the Doctor out. Rory, who can't comprehend how careless the Doctor is when it comes to choosing his spots for adventures. Rory, who, with his honest, straightforward mind, would likely, if he had control of the TARDIS, only take the people with him to places where he could be sure they wouldn't fall to harm. He would protect his companions properly; that's just the sort of person Rory is.
Sitting at the controls, listening to the background noise of the TARDIS and the soft breathing of two sleeping humans, the Doctor wonders if Rory had meant what he had said. Whether it was just something said in the heat of anger or a true reflection of his thoughts, it still hurt to hear it. The Doctor isn't just going to toss someone off his TARDIS for that, especially not if the speaker is Rory. If the Doctor got rid of Rory, Amy would insist on leaving too and that…
That's just not a situation the Doctor can endure. Amy and Rory are the only consistent companions he has had in this form, and they are essentially what the Doctor thought he would never have again, not after Gallifrey. They've become his family in everything but name, and given the way his relationship with River is progressing even that may change in the future. The Doctor doesn't know or like to think of what he would do without them, not now.
So of course, he won't make either of them leave. How could he possibly do so, especially now when they are still searching for baby Melody? These little trips they've been making since Berlin have only been side trips, breathers, in the search for Melody, when neither the Doctor, Amy nor Rory have quite been able to bear bringing her name up even in passing. How can the Doctor possibly make them leave now, even knowing that he's slowly, unavoidably ruining their lives, just like he did with every companion to come before?
That woman, that woman whom Amy became (never should have become), waiting thirty-six years for saviors who never came.
"I hate you. Do you hear me, Raggedy Man? I hate you more than anyone I've ever met."
When the Doctor looked at her through the glasses he gave Rory, he could never quite bear to see her. He didn't like to think of all the ways thirty-six years completely alone except for a computerized voice and a handless robot was capable of changing Amy, even if it wasn't his Amy. He didn't like to think of the message Rory found, in red ink, long since faded. He didn't like to think that this was his fault.
Rory was appalled at what had happened to her, and why shouldn't he be? Amy is his wife; the thought of the woman he loves being totally alone for as long as she was ought to appall him. The Doctor knows, however, that there is a deeper reason for Rory's horror at discovering the fate of the older Amy. Rory waited, guarding a box, for just over a century shy of two thousand years, alone. The only company he ever had was the company of those who wished to steal the Pandorica, and he always had to drive them away. Rory's wait was far longer and infinitely harder than that of the Amy who was left behind, but what it did to her…
As much as the Doctor hadn't wanted to look at her, there had been no avoiding it when their eyes locked, from across the room.
For a moment, all the hate dropped out of that old, tired face. For one shining moment, the pretense of hatred and bitterness was completely gone and the Doctor could see someone far younger and happier lurking in that weary body. Hope transformed her face, and the Doctor could almost his Amy, his Amy, beneath that face devoured by despair.
You came. You finally came for me.
Then, the moment passed, and the Amy who should never have been realized exactly what was about to happen.
She dropped everything she was holding and ran. She ran so hard, so fast, the hope vanishing from her face all the while.
And at the very last moment, the Doctor slammed the door in her face.
"There can never be two Amys."
The Doctor wouldn't let Rory be the one to make that choice. He wouldn't let Rory be the one who slammed the door in her face.
He's taken the choice away from so many people, so many times. Not just now, but in dragging a screaming Amy from Rory's corpse a universe ago. In taking Donna's from her so that she would at least live, even if diminished. In not giving Rose and the half-human Doctor the right to stay in the universe, after Rose came so far to find him. Taking these cruel choices from them is an act of cruelty in itself, but the Doctor knows that the alternative is far worse.
These humans, these small, frail creatures, they burn out like old, decrepit stars under the weight of all their choices. Their despair, their guilt, their aching, longing pain, it crushes them utterly. The Doctor has watched so many fall that way, watched them drown in their own heartbreak. No more.
The Doctor makes all the cruelest choices. He loves them, all of them, too well, too deeply, and he makes all the cruelest choices because he knows they would break under their weight. He knows they would break, and can't bear to watch, knowing it would be his own fault. Even if they hate him for that, he can't stand to watch them break.
So he breaks for them, instead.