Smiling nonchalantly at Amy as he returned to the TARDIS, trying to push the current questions about the Pandorica- whatever that really meant, since it almost certainly wasn't what the tales said- and the temporal explosion he'd detected to the side until the opportunity came to learn more about them, the Doctor casually walked up to the console and set the controls in motion, smiling slightly as he felt the TARDIS return to its natural environment of the Time Vortex, thoughts of the future pushed aside as his ship returned to its rightful place in existence...
"It's making the noise," Amy said, walking up to stand alongside the Doctor as she looked curiously at the console before her.
" 'course it is," the Doctor replied with a nonchalant glance at Amy. "I told you, I love that noise."
"But if you're keeping the brakes on-" Amy began.
"I'm not," the Doctor said simply.
"Pardon?" Amy said, looking at him in confusion. "But... why did River say that's what caused it?"
"Because I told her that's what does it in my future so she'd do it then," the Doctor said, inwardly cursing his future self even as he apologetically patted the TARDIS console as it continued its transition back into the vortex; the 'wheezing' was taking longer than normal, but after being forced so abruptly out of its environment the ship was entitled to take its time. "She'd already done it and told me that was why she did it, so I decided to do it that way because it had already happened; keep the timeline straight-ish, you know how it goes."
"Oh," Amy said, nodding in a confused understanding- not that he could blame her; the anomalies of River's life with him were enough to give him a headache, and he'd dealt with Faction Paradox- before she looked at him more curiously. "So... if she wasn't putting the brakes on... what did she do?"
For a moment, the Doctor thought about avoiding that question like he had so many others, but the memory of the various unanswered questions left for them after this recent mess with the Angels pushed any thoughts of deception aside; he and Amy had enough questions to answer about what was happening to reality without them factoring in anything they might not be telling each other.
"Well, that's the thing..." he said, looking uncertainly upwards for a moment before he looked back at Amy. "You see, the TARDIS is alive, Amy-"
"Alive?" Amy repeated, looking at the ship around her with a sudden unease. "As in... alive alive? Like the star whale?"
"Bit further along the evolutionary line than that, but yeah, pretty much," the Doctor replied, smiling briefly at that memory- it was moments like that incident that made him glad that he'd managed to convince her to travel with him after that whole mess with the TARDIS repairing itself after his last regeneration (He'd have to be sure not to repeat that mess next time it happened; saying goodbye to everyone was one thing, but hanging on for that last visit to Rose had really been pushing it)- before he continued. "Anyway, the thing is, when I first left home in the TARDIS... well, things were a bit complicated and I was in a bit of trouble with a few people, so..."
"You stole it?" Amy finished, unable to stop a slight smile as she looked at him. "You bad boy..."
"It's not like it was the latest model- she'd probably have been scrapped if I hadn't stepped in-, but the point is..." the Doctor began, before he sighed slightly as though thinking over what he was about to say before he continued. "Anyway, normally when Time Lords go anywhere in their TARDISes, they get around by forming a direct mental link with the ship to direct it wherever they want to go; saves on having to actually worry about remembering precise coordinates when they can just 'will' the ship to go wherever they want..."
"And... you do all this... running about and flicking switches... because...?" Amy asked, waving a hand promptingly.
"When Time Lords pilot their TARDISes that way, they leave a telepathic trace of where they're going that could be tracked back on Gallifrey," the Doctor explained. "Instead of forcing my mind onto hers and controlling her more directly through the telepathic link, I built my own controls to handle her, bypassing the usual symbiotic relationship that I'd have with her and creating a more physical approach to piloting her; it's a bit cruder, but essentially it means that, instead of me willing her to go where I want, most of the time in the early days she just went wherever she wanted at random; it took some time before I got a good handle on getting the controls right to let her go where I wanted to go without forcing anything-"
"Uh, not that this isn't fascinating- and slightly strange-, but what does this have to do with River?" Amy asked, holding up a hand to stop the Doctor's explanation.
"In a nutshell- and that's always been a strange phrase to me-, I escaped the Time Lords by allowing the TARDIS her freedom to basically go and do whatever she wants at her own pace unless I really need to get somewhere; it's one reason I have a bit of trouble with her at the moment, she's still straightening herself out after a bit of an... accident... we had before I met you," the Doctor explained, before he leaned over to place a hand sympathetically on the console. "What River did..."
He shook his head in disgust. "What she did basically forced the TARDIS out of the Vortex instantly by taking its own mind completely out of the picture."
"And... that's bad?" Amy asked.
"Think of what happens when you jump in a pool of practically ice-cold water all at once and then compare it to being allowed to walk in at your own pace," the Doctor finished for her.
Amy couldn't help but shiver slightly at the memory of a time when she'd done that.
It might not hurt, but it wasn't exactly... comfortable...
"And... what's that got to do with how the TARDIS lands?" she asked, looking at the Doctor in confusion.
"What River did to the TARDIS is the equivalent of her making you jump into the cold water rather than easing its way out," the Doctor explained. "When it makes the noise, the TARDIS is doing the equivalent of easing itself into the cold water of the real universe and out of its natural environment of the Time Vortex; it can survive in both easily enough, but the controls essentially help it go from the vortex to our universe while making sure it's comfortable."
"Oh," Amy said, nodding slightly in understanding before she looked at him in confusion. "But... if she's your wife...?"
"She's not," the Doctor said simply, turning his attention back to the controls. "I don't know what she is to me in the future, but she is not my wife."
River might have left him with a multitude of hints, unanswered questions, and almost more innuendos that Captain Jack Harkness could manage in the same amount of time, but he knew one thing for certain; she was not, and never would be, his wife (At least not by any standards that he would recognise; he might have to do something in the future to ensure that it worked out that way from her perspective).
He'd been fairly certain about the truth ever since she'd whispered what she'd evidently assumed was his name to him- the fact that she'd known any Gallifreyian had been enough to confirm for him that she'd known his future self, even if the phrase had made little sense in context; hi 'gambit' that it had been what she thought was his name had paid off at the end-, but it had been her reaction to his offer to change history when she was about to sacrifice herself that had been the confirmation for him.
"Not those times. Not one line! Don't you dare! It's OK. It's OK, it's not over for you. You'll see me again. You've got all of that to come. You and me, time and space. You watch us run!"...
It had all been about her.
She hadn't said a single word about the people they'd saved together- and they would have saved people together; he couldn't travel without saving people-; she'd only wanted him to preserve her past because of what she had seen with him.
Travelling with him might be an incredible experience, but if Doctor/Professor/whatever-her-title-was-now River Song had thought that it would convince him to leave his future with her intact by talking about what they'd seen together rather than talking about what they'd done together, then she'd clearly missed the point of going with him.
The fact that she'd been sentenced to prison might be a potential problem, but it was hardly like he was in a position to judge anyone for being in prison after all the prisons he'd been sent to and escaped from over the years- it seemed like he'd escaped from every kind of cell and prison, ranging in quality from Colditz in his seventh body to that mess with the Oliver Bainbridge Functional Stabilisation Centre in his eighth incarnation-; the question of why she'd killed that man- whoever he was; after her comment about knowing someone who could pilot the TARDIS 'better' than he could, it was clear that there was more going on here than he knew yet- was another issue that left him increasingly doubting her.
Even if she'd had to kill that man for some reason or another- and he'd certainly been in positions like that often enough; he still wished he'd been able to find another way to stop the Sirens of Time without condemning the Temperon like that-, she hadn't even seemed that sorry about it; murder was not something you could be nonchalant about it.
When adding in her arrogant presumption- even in a panicked condition- that she might actually be a space-time event of sufficient complexity to overfeed that scar in reality...
It wasn't that he didn't appreciate his companions being confident, but there was a difference between confidence and arrogance; how could a woman who claimed that she needed to be so careful about 'spoilers' be so utterly casual about asking him where they were in their relative timelines, followed by her casual reaction to the idea that he might have something better to do than save her...
The 'secret' his future self had told her had been correct; she really was crazy, to an almost messiah-esque degree of self-centredness...
God... he groaned mentally, staring upwards at the ceiling. And there was me hoping that Faction Paradox would be the worst temporal paradox I'd have to deal with in my lives...
Like this whole mess with the cracks in reality and the potential temporal explosion that had caused those cracks wasn't enough for him to be dealing with; even after that was all over, he'd still have to deal with the issue of a companion he didn't want, who may or may not have murdered someone and was simultaneously delusional enough to make their relationship some big thing that it wasn't even close to being in reality...
He might not have the full picture yet, but the more he learned about the complete picture, the less he liked about the woman it presented; the arrogant presumption in their first meeting that he'd have to be a Doctor who knew her when she should know that there were at least nine of him that she could never meet...
"I wanna go home," Amy said as the TARDIS completed its transition back into the vortex.
The Doctor couldn't help but feel slightly hurt at that; he'd really thought that he and Amy were connecting- it wasn't every companion who waited for him for the better part of fourteen years, after all-, and now here she was, leaving after only a few stops...
"OK," he said after a moment's pause, reaching over to set the controls.
He'd just have to see about finding someone else after she was gone; maybe Lady Christina might be open to the possibility of another trip if he apologised for his abrupt dismissal of her in their last meeting...
"No, not like that," Amy said, breaking into his train of thought with a brief smile as she walked up to stand beside him. "I just... want to show you something."
Curious, the Doctor turned to look at Amy, noting her slightly apprehensive manner as she stared back at him, clearly uncertain about what she was about to say, before she spoke again.
"You're running from River," she said, looking solemnly at him. "I'm running too."
The Doctor didn't know what Amy meant by that last comment, but he had a feeling that things were about to get very interesting...
AN 3: Just to clarify, I'm assuming that what River whispered to the Doctor in "Forest of the Dead" wasn't actually his name, but simply a phrase in Gallifreyian- which, roughly translated, would mean something like "Humour me; I'm crazy" (The principle's kind of like in the Tintin tale "The Blue Lotus", where a warrant for Tintin's arrest in Chinese was replaced with a piece of paper that said on it in Chinese "In case you hadn't noticed, we are lunatics and this proves it")- that sounds like it could be a name to someone who doesn't know the language intimately; it would confirm for the Doctor that she has had contact with his future self while also giving him an idea that the relationship that she believes she has with him is not the same as the relationship he will have with her...
Might be harsh, but the more I see of River Song, the more I become convinced that the Doctor would never see her as more than a frustrating acquaintance at best even if they met each other in the right order (As in, with her first meeting at the Doctor being the same as his first meeting with her, rather than him meeting her at the moment of her 'death'); as it is, everything about his 'relationship' with her is tainted by the fact that he has to set things up so that she's in a position to save everyone in the Library, and is hence really questionable even without this latest news that she killed someone...