Take note; this is not Doctor-bashing. Something I've noticed in the characterizations of the Ninth, Tenth and Eleventh Doctors is that they seem possessed of more than a hint of self-loathing. I just make that come across here.
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Maybe Rory's incisive, uncomfortably truthful comments were starting to get to him, or maybe the Doctor just had one of those heartbreaking moments of clarity that he tried so hard to avoid, but when he saw that little girl, sitting on top of a suitcase in the hotel room, the Doctor knew there was only one way to right this situation.
The control room of the TARDIS is far quieter than usual, and noticeably more dimly lit. If it's a question of the lighting, it could be a gentle prodding on the part of the TARDIS, telling him that it's very late and that even if he doesn't needs as much of it as humans, Time Lords need to sleep too. The TARDIS does tend to do that from time to time, worrying about him in an almost motherly fashion. As for the quiet, as for the resounding silence…
It's just the Doctor here now. Even when he talks to himself or to the TARDIS as he's wont to do, without Amy and Rory there, it's not going to be as full of life in the control room as it usually is.
When he first got the idea into his head, when he first decided that it had to be done, the Doctor could not help but be reminded of how disastrously things tended to end up when he was by himself. There is a danger, the Doctor realizes, in traveling by himself, without anyone there to stop him. Mars and Bowie One immediately springs to mind, the tragedy, his mistakes, and the drastic measure taken to make sure that nothing would change.
Doubt is shaken off soon enough. This has to be done.
Amy took it far better than the Doctor expected—the level of grace she displayed upon realizing that he was about to leave was humbling, even if she was near tears the whole time. A hug, a chaste kiss, instructions to tell River to visit if he ever ran into her, and no bitterness. Amy wasn't like Rose or Donna; she never expected it to last forever. He swore he would come back, and given the number of times the Doctor has crashed into her life, Amy believed him. And the Doctor will go visit, it's just…
I can't let it happen again.
The Doctor took care to beat it before Rory came back. Rory would have only, and not without justification, gotten angry or at least indignant to know that the Doctor didn't want to at least say goodbye properly. Perhaps as a result of his days as the last Centurion, Rory prefers to do things properly; no skimping or corner-cutting for the Roman.
He left them, taking off in his magic blue box just as Rory came back outside with a wine bottle and a couple of flutes, and now, the Doctor is all alone, once again. The Doctor, in the TARDIS, with no one for company but the ship herself. Alone, the corridors so quiet that he's seriously starting to contemplate breaking out a stereo and putting on some big band music just to liven up the scene.
It's for the best, he keeps telling himself, a salve to self-inflicted bruises that really doesn't help at all. Leaving Amy and Rory behind stings. They are the only true companions the Doctor has had in this incarnation; their presence has been one of the few constants in his chaotic life since his last regeneration. They've become something like his family, in a way that goes deeper than what the Doctor had with most of his past companions. The Doctor has gotten to the point that he doesn't particularly want to imagine his life without them, even knowing that whatever happens, he'll outlive them, and that… The Doctor swallows hard, and nods, trying to convince himself that this is right. That's why.
"Why now?"
"Because you're still breathing."
That's the rub. That is the most important thing about it.
When the Doctor knows he's heading into danger, knows he's facing a foe that could potentially and his life, put the Earth at risk, or even threaten all of reality, he often so recklessly brings his companions along for the ride. Frail humans, so good, so kind, so brave, but their bodies are fragile, and if the Doctor cared a little more for their well-being, he would never have put them at risk.
How many lives has he put at risk through his own suicidal recklessness?
Rose absorbed the heart of the TARDIS because she "wanted him safe". Granted, this time, even if it was only this time, the Doctor at least tried to keep her out of harm's way, but when he looked at her, at what she had become, and how both she and the Bad Wolf were burning, that wasn't what he remembered. He only remembered that he hadn't been firm enough, that she had done this for him.
Later, Rose came within a hairsbreadth of ending up in the Void with the Daleks and the Cybermen, and would have spent an eternity in the Howling if not for Pete's intervention. She had come back to that universe to help him but the Doctor should have known better than to let her stay. The Doctor should have sent Rose back to Pete's World but he didn't, because in his selfishness, he wanted Rose with him. He had tried to deny it, but the reality is that that's what the Doctor wanted, more than anything.
Jack Harkness started out as a loveable if just a touch cowardly rogue. Time with Rose and the Doctor soon cured him of that, but being made immortal by Bad Wolf didn't do much for his happiness.
"I was hoping you could… fix me."
After spending decades as an immortal all Jack wanted to do was die; where once the core of his being was levity, the bitterness in him was unmistakable. The Doctor had finally found a kindred spirit but thanks to his species' ingrained prejudice against immortals he could not get past the deep-seated feeling that Jack's whole existence was wrong, and went out of his way to avoid him. Jack and Amy could have a long conversation about being abandoned multiple times by a Time Lord in a magic blue box.
Martha spent a year walking the ruined earth, on the run from the Toclafane during the year that never was. Though he never asked her to kill or even to pick up a weapon, the Doctor turned her into his soldier, and she fought for a man who never noticed her the way she wanted him to. Her family played captive to the Master during that lost year and were tormented nearly beyond their capacity to endure it. Only later, watching her work with UNIT, did the Doctor realize just what that year had done to her, just what he had done to her.
River died in the Library the first day he met her, grieving terribly over a relationship lost that the Doctor hadn't at the time even known existed. Up until the moment she whispered his name in his ear, the Doctor hadn't even thought River was telling the truth about knowing him from the future; he'd just thought her to be a madwoman or a con artist with some lucky information. Since then he's treated her insensitively and been at times downright cruel, all the while finding himself more and more attracted to her, up until the day he realized that, before even meeting her he had put her life completely in shambles.
And Donna. Donna's rueful fate, the Doctor would not wish on anyone.
Under his "care", Rory and Amy have come so close to death so many times. Hell, the objective of most of the foes they face seems to be to either beat Rory up or kill him; usually it's the female of the group who's the designated victim, but apparently Rory just has "punching bag" stamped all over him in invisible ink, or something. Maybe he's giving off some sort of pheromone that tells all monsters in the vicinity that he's fair game. Less humorously, the Doctor can not remember them ever taking a trip where Amy and Rory were not nearly killed, hurt or at least threatened. This is par for course, but he's become more keenly aware of it since Demon's Run.
"How far you've come."
He invites danger everywhere he goes. The Doctor doesn't even have to do anything at all anymore to be shot at, threatened or imprisoned. And Amy and Rory are always right there, getting caught in the crossfire.
That's why. When the Doctor left them they were still alive, relatively whole and sane—that's a lot more than can be said for a good many of his past companions. They are hardly unchanged or unscarred by their experiences, but they still have a chance to lead a somewhat normal life. They have an apartment, and even a new car; the Doctor nearly laughed at Rory's positively ecstatic reaction to seeing a sleek, shiny red car parked in front of his apartment.
The Doctor can't remember the last time a companion left the TARDIS without there having been some sort of horrible trauma or them dying first. He knows it has to have happened at least once, but in all honesty, he can't remember.
When the most immediate danger has passed and things start to quiet down again, maybe then the Doctor will find some lonely, some dissatisfied soul somewhere and take him or her for a few fun trips. To places where there are no alien plagues, no genocidal aliens, no dangers. Then, and only then. Never again, the Doctor tells himself, will he take his companions into the jaws of Hell; never again will he deliberately take them into the unknown, knowing that there is naught but danger waiting at the other end.
He knows better now. He knows that he doesn't have the right to play God, or put his companions' lives at risk.
"It's time we saw each other for who we really are."
Amy's faith has never wavered, but the Doctor knows that he has never deserved anyone's faith less than he does Amy's. He has abandoned her so many times, granted not always on purpose, but that does little to lessen the impact it had on her psyche. She spent fourteen yeas waiting for her imaginary friend to come back to her, and her faith never wavered.
Faith. The Doctor snorts. If Amy wants to have faith in someone, she ought to have faith in Rory. Rory will never leave her, never hurt her, never leave her waiting for fourteen years with only a memory to sustain her. Rory will love her and protect her to the end of the universe; it's never even occurred to him to act differently.
No. Even if it hurts, even if Amy is better for finally having had a childhood promise fulfilled, she's better off with her Raggedy Doctor out of her life. A few visits now and then, but out of her life. He doesn't deserve her faith, he keeps leading her into danger, he once left an older version of herself alone for thirty-six years…
"I wasn't talking about myself."
…and the Doctor is seriously starting to wonder whether he isn't poison to everyone around him.
The Doctor had been talking about the Minotaur; he will maintain that to the end of time, even when his face pales a touch and his eyes scan the floor or the ceiling instead of making contact with anyone else's. The Minotaur, however, thought differently.
"It's sad," comes the faint, yet still guttural voice. "You have so many wonderful things in your life, and yet you still want to die."
Still maintaining that he wasn't talking about himself, the Doctor starts to think. "An ancient creature, drenched in the blood of the innocent, drifting in space through an endless shifting maze. For such a creature, death would be a gift." Would it? Would it really?
The more the Doctor thinks about it, and what his answer might be, the more frightened he becomes.
And, no longer trusting his own intentions, he is glad he broke Amy's faith in him.
It would have gotten her killed.