Obligatory Disclaimer: Inspired by, dedicated to and in the greatest respect of Doctor Who, Torchwood and especially David Tennant, for whom I wish nothing but the best as he moves on.
"Forgive, and ye shall be forgiven."
Standalone but follows my story 'Solipsism'.
Wil began drawing imaginary figures on the cement with her finger. "Subspace is a common enough concept in linear algebra describing sets of closed vectors."
"Right, linear algebra," Jack muttered; Wil ignored him and went on as The Doctor smiled.
"But string theory uses the concept, too. It tells us that there are more than four dimensions – at least ten – and probably more, that may or may not affect us and that we may or may not perceive. Subspace, if it exists, lies within the boundaries of these other dimensions and is, for all intents and purposes, disconnected from us. It has a different set of physical laws and, indeed, I might postulate that there could be multiple, perhaps infinite, subspaces with a variety of physical laws. Some researchers have hypothesized that there may be life forms occupying subspace, but that is conjecture, as is, to be honest, string theory and the concept of subspace itself." 
Finally he noticed the cello and music stand that were resting against the wall. At first he scoffed, but then realized they'd been safely secured with small straps. Bless her; Wil had made them TARDIS-proof!
As he wandered from room to room he gradually perceived there were shelves and nooks and crannies everywhere filled with musical instruments. Not only earth instruments from various cultures and time periods, but music devices from many different planets, including numerous exceedingly curious objects he'd never seen before.
He smiled and then he laughed out loud.
Walking over to a shelf, The Doctor took down what appeared to be a Stradivarius reproduction. Or was it the real thing, he wondered. Regardless, he thought, it was a lovely violin.
He held it tenderly to his left shoulder, picked up the bow, and began to play. 
She noticed The Doctor beginning to stir. Gently she reached out with a small corner of her mind and prodded him. The Time Lord tentatively touched her back. He was weak, but he was okay. She smiled inwardly and then shrugged, refocusing complete attention on her internal discussion.
"But I'm not through, not yet. I have one last demand," Wil said silently. "I want to know something. I want you to explain why now. What caused you to take your leap at this time? You weren't ready – you aren't ready – yet something unusual must've set you off, something unnatural sped up a process that should have lasted another thousand years, if not a thousand millennia. What was it?"
When the voice inside her mind finally concluded its surprisingly long response, the human part of Wil Beinert squeezed her eyes shut and silently mouthed, "Oh no." A single tear ran down her cheek.
"I'm very sorry," the voice replied sadly, sounding like it meant it. 
 "Terraform" Chapter 7.
 "Plague" Chapter 23.
 "Abomination" Chapter 36.
"Yes, Grasshopper?" Wil Beinert always smiled inwardly at the moniker she'd bequeathed upon her TARDIS. At first it had been a private joke, but of course eventually she explained the significance of the name, told the story of Kwai Chang Caine and Master Po. It was among many of the fictional tales she had related to the ship during their time together. Some of the stories were just for fun – fairy tales and fables – not all were entertaining as well as instructional and portentous like the saga of Caine, the boy who at first could neither hear his own heartbeat nor the grasshopper at his feet.
"May I ask you something?"
There was a long pause.
"What is it, Grasshopper?"
"The question may not please you."
"Ah. A candle cannot burn without fire. Be so good as to ask your question. Pleasing me should not be a concern."
"What if I told you, Teacher, I need to return?"
"Return to where, Grasshopper?"
"To the universe of my origin."
Now there was another deep silence. So soon? Wil thought, and then dispelled from her mind the rapidly descending shadows. She'd always known that one day the TARDIS which had fallen into her life and under her care would make this request, though she'd believed she would have more time. But wasn't that the way things always went? She had been given the time that she was given… Whether it was sufficient wasn't part of the equation.
"Then I would tell you that you must go."
There was another long pause. Wil waited patiently.
"But I am afraid, Teacher."
"Of what, Grasshopper?"
"Of making a mistake."
"The only mistakes to fear, Grasshopper, are not starting your journey and not finishing it. You have already accomplished the former, and you have traveled well. I have faith in you, Grasshopper. And I am proud of you. You have learned exemplarily what I have taught you."
Wil felt the warmth of her approval radiate back onto her. But there was more there than simply that. She also felt the attainment of potential. She felt the confidence and serenity of her student. She felt virtue and even – thank the stars! – humor.
"I have the best Teacher in this universe or any other," was the response. "My Teacher taught me to avoid, rather than check. Check, rather than hurt. Hurt, rather than maim. Maim, rather than kill. For all life is precious, nor can any be replaced…"
"Indeed, Grasshopper. You have shown me that you see clearly not only what has been done but what remains to be done. That you understand that you find yourself by looking within and not without. That you know we must not only seek to learn the answers but to always understand the questions as well. And now I have a question for you.
"As a TARDIS you do not exist solely in one universe. You have always had the ability to return. What you lacked was the wisdom to persevere. But that is no longer the case. My question is: do you want me to come with you?"
Two men were hiking across an immense field on an unknown planet, in an unnamed solar system of the Eris galaxy.
The taller of the two was wearing a long, dark blue greatcoat, the origin of said garmant was a watery, marbled world physically thousands of light years away, and psychologically more distant still. He strode along with the studied assurance of a strong, self-confident man, the unbuttoned coat flapping around his legs. His dark hair contrasted with his shockingly bright blue eyes, and he had a couple of days' worth of beard growth on his face.
The other man was smaller, slender and pale. But it would be a grave error to mistake him as weak. He moved like a feral animal and his gray eyes were constantly surveilling the surroundings, although he was well aware there was nothing even remotely dangerous anywhere on the isolated planet which had become their temporary home.
"So Jack, can I ask you something?" the shorter man's voice was somewhat breathless with the swift pace.
"Ask away, John." The response was less winded – but granted, longer legs were at work here, not to mention the respondent was probably a tad more fit.
"You've told me that you weren't exactly out looking for me," when Captain Jack Harkness motioned as if to interrupt him, Captain John Hart waved him off. "And that's okay, really. I totally understand you had no reason to be worried. But that being said how was it you showed up when you did, where you did? I mean…"
"You mean…" this time Jack was successful in disrupting his friend, "of all the gin joints, in all the towns, in all the world…?"
John pulled a face, "Huh?"
"Never mind! You are asking how was it we ended up here?"
"I don't have a decent answer to that question, although I admit it is a very good question indeed. The Doctor and I were totally intending to travel somewhere else. What we wanted to do was hunt Dyson spheres. Instead, as it turned out, we materialized in this solar system, just off the port bow of a shockingly derelict Time Agency ship, the Newhope. At first we had no idea she was even out there, floating in cold dead space. Nor did we know that you were inside, waiting for us to find you and thaw you out of hibernation."
"Dyson spheres? Hunt?"
"Stay focused; and keep up with me, would you, John? We're hiking, not strolling."
"Sorry, Jack. What's a Dyson sphere?"
"Forget it, John. It's nothing. The Doctor hasn't spoken of our unexpected detour again, but I suspect the TARDIS brought us here intentionally. It's the only explanation that makes any sense. She must've somehow known something had gone wrong. God knows how. We know she had some sort of special relationship with the Newhope. Could that be it? But you've had as much contact with the TARDIS as anyone these last few days. Hasn't she told you anything? Have you even asked her?"
"Me? No… But our communication is pretty much in one direction. She tells me things when she needs to, but I don't really have a good way of asking her questions, and she's not… well… she's not the chatty type, if you know what I mean?
"But speaking of The Doctor…"
At this Jack stopped and turned to glare at his friend, his former partner, his sometime lover and occasional rival. "What do you want to know about The Doctor?" he scowled.
John would not back down. He'd known Jack too long to be susceptible to that particular flavor of Harkness intimidation. "What's going on with him, Jack? I've hardly seen him and when I do, he doesn't appear well. Is something wrong?"
Jack's eyes darted around, quickly taking in their environs. The TARDIS was several miles away, her Time Lord ensconced securely within. And yet the Captain still felt himself not trusting what he could say out loud. It wasn't John, per se. He trusted John Hart as much as he trusted any other human. And the planet itself was as benign a world as could be imagined. Moreover one would have to travel thousands of parsecs from their current location in order to bump into any sort of sentient life. There was absolutely nothing rational about the disquiet and suspicion he felt permeating his soul, but neither could it be denied.
Nevertheless Jack felt an irresistible longing to share the growing darkness he'd been hiding within. He slowly brought his hands up to John's face and as their eyes met and locked, he kissed John passionately. He then languidly, exquisitely moved his lips to John's cheek, eye, and finally to his ear, where following a deeply sensual kiss he whispered his answer almost soundlessly, "I don't know."
After a long moment John pulled back ever so slightly and in turn whispered in Jack's ear, "You need to shave."