River Song had all the time in the world. She had nothing to do but read in peace and quiet. So she did, for several centuries, reading in the peace and quiet of a planet scale Library devoid of all life except for the swarm of billions of flesh eating mites known as the Vashta Nerada. The Library was devoid of all life, including our unfortunate Dr. Song who was not 'alive' as we know it but rather 'saved' into The Library's central computer. There she continued a virtual existence along with a few others who had been similarly saved and the little girl Charlotte Abigail Lux for whom The Library had been built as a home and cybernetic body when she was dying of a tragic childhood illness.
River Song had all the time in the world, and she meant to use it. After getting over the initial shock of having died and been saved she realized she had been given an unusual gift. In her new virtual existence she was virtually immortal, The Library's systems would carry on automatically for many millennia more, and she had The Library. While not as advanced as some sciences she had seen out in the universe, its catalogs were extensive and there was much to be learnt. The only catch was that to make use of what she learned she would have to figure out a way to get out of The Library.
River Song had a mission: learn all that could be usefully learned from The Library, including, and especially, how to reconstitute herself into a body and escape The Library.
The Doctor felt a tingle in his breast pocket. Something was trying to get his attention. No, not the Sonic Screwdriver, that was in a different pocket. How many pockets does this coat have? Oh, right, 5137. (Time Lords, especially Time Lords with peculiar rebellious affectations, even made their coats bigger on the inside.)
The Doctor thought to himself (having no one at the moment to talk to about how terribly clever he is), "I don't think I've reached into this pocket yet, not in this body anyhow. I guess I'll just have to remind myself what's in there by checking."
Psychic paper! And it's received a message!
. . . . .
Space time coordinates. In Gallifreyan.
This was, of course, impossible.
There was no one, alive, in this universe, who could have sent that.
He was still adjusting to this body, but his previous two ached out for who it might be, and all thirteen of him feared for what else it might mean.
On the down side, it could be a Dalek or Cyberman trap. They had gotten frightfully clever lately. It could be a Time Lord, perhaps one had figured out to squeeze back into this universe from wherever Gallifrey had gotten exiled. Maybe not all the Time Lords, but maybe just one.
It could be The Master, who has seemed to die several times only to come back. For all the battles they've fought The Doctor would be a little bit glad to have the company of a Time Lord again, even if it was his old adversary.
It could be his clone 'daughter'. No idea where she would have managed to learn Gallifreyan, but coming from his clever stock no doubt she could manage it.
Or it could be River. His love, his wife. Dead. She had died, as he saw it, the first time he met her. It hadn't meant so much then, seeing someone you just met die, that happens sometimes. The Doctor leads a dangerous life. He tries very hard but doesn't always succeed. Sometimes he has a very good day and everybody lives. This day his future self had been very clever and found a way to save her into the data banks of The Library, and his self then did it and saved her. Everybody lived.
But over the years and meetings he had grown to love her, and all the while he had to hide that he knew. (And somehow all the while he was meeting her and growing to love her, she had hid from him that they were married, right up to the end.) Then, at the end of the universe and the end of time (one of them), they were married.
He thought that all of her timelines were closed off to him and he would never meet her again. All of her days had happened in some way causally linked to his own timeline now, with enough meetings and crossings, and there was no way to go back and see her again. He had lost a few people that way, someone just had to say, "The Brigadier so hoped to see you before the end", and it was done. The Doctor knew that it hadn't happened and now it couldn't happen. He couldn't go back and change events to change that sentence he had just heard. He lost the Ponds to the past and the Weeping Angels and only got their farewell letter in a book they published. He already had the book; it had already happened; it was the past closed to him.
The Doctor spent a moment weighing the possibilities and the hopes and fears. But after a moment he leapt into action and started punching in the coordinates and throwing levers to get the TARDIS on course. The message was impossible, and nothing gets The Doctor moving like the impossible.
The first bit of good news River found was that the Vashta Nerada hadn't touched her old body. It was not quite habitable though. It had been fried and overloaded during her heroic act of self sacrifice getting thousands of people off planet who had been trapped in The Library's computer memory since the start of the Vashta Nerada infestation a century earlier. But her heroic act of self sacrifice saved one life even more important to her, The Doctor. If she hadn't done it, he would have. And she knew his future and knew he had to go on and save millions and billions more. Maybe The Doctor can save everyone, but who can save The Doctor? She can. Twice. River thought a little smirking smile to herself at that.
Her old body was not quite habitable or reparable, but she could get good scans of it. There were certain features that she absolutely must reproduce if she figures out how to build a new one. Some part of her did feel a moment of squeamishness at analyzing her own corpse (not many people get a chance to do that!) but then the scientist in her kicked in and she got down to work. The Project was underway.
The Doctor recognized a bit of the coordinates as he was setting them in the TARDIS. The Library, but over a thousand years after the last time he had been there. Hope was getting to him now. He was either going to meet River there, or be very cross with whoever was baiting him and disturbing her grave.
He threw one final lever and the TARDIS groaned to life, dematerialized, and got underway.
River's old body was not reparable by any known medicine. She knew. She'd read it all. But just in case she had preserved the old cadaver the way all the old patrons of The Library had been saved when the Vashta Nerada first came. She transmatted it but redirected the signal into the computer memory of The Library. That had been over two hundred years ago now, but it was still perfectly preserved as information checksummed and error-corrected in computer memory. It was an immense amount of information, preserving the atomic states of an entire body (living or otherwise), but The Library was designed with immense computers, storing all knowledge then known and with room to spare.
Dr. Song (now eligible for an M.D. from all the medical texts she'd read) started looking at this data directly. Atom by atom, nanometer by nanometer. She took a 89 year diversion to read up on computer memories and atomic physics. Then she made a backup, and started making a few edits. This was intensely detail oriented work. No one would ever undertake medicine on the atomic scale this way. It would take hundreds of years to heal the patient, by which time everyone they had known would be dead. No patient would submit to such measures and no doctor (or team of doctors, each spending perhaps a lifetime of 60 years on the project) would do the work. But River song was both the doctor and the patient, and she was quite patient. She had all the time in the world.
River's old body was not reparable by any known medicine, so she invented a new one.
The TARDIS materialized well outside the atmosphere high over The Library. The Doctor, two lifetimes ago, had promised the Vashta Nerada that he would never come back to the planet, and for the moment that was true enough. The TARDIS stopped and nothing happened. The Doctor scanned the planet and its Moon, all seemed just as he had left it.
This mystery was not going to give itself up just yet. The Doctor waited. The Doctor hated waiting.
River started small. There was no where else to start. At first she tried to fix just one cell. She transmatted it back into physical existence and watched it live and die over the course of a second, a lone animal skin cell without a body and exposed.
It was a success. Fixing the rest was just a matter of time, perhaps eight centuries or so. Now she just had to get a message out so that her Sweetie could swing by and pick her up.
The phone rang. The Doctor was at once startled and really glad he had patched the phone back into the main console last week so that he didn't have to reach out into space over a planet infested by Vashta Nerada just to answer the phone. He also considered that he ought to stop giving out his number given the amount of phone calls he had been receiving recently. He also considered that he never gave out his number and it wasn't a real phone and he looked askew at the ringing phone and thought that maybe the TARDIS had a sense of humor. It had once told him that it always took him where he needed to go, and perhaps it had a way of also getting him phone calls he needed to take.
The phone rang a third time and The Doctor dove into the mystery of the ringing phone with his usual style of direct examination. He picked up the phone, "Hello?"
A smooth, reassuring voice answered, "This is Dr. Moon speaking. In my capacity as a doctor I am on an errand of mercy to deliver you a message. If you will lower your shields, we can talk directly."
"Dr. Moon! It's been a long time! How have you been? How's little Charlotte Abigail Lux?"
The Doctor's jovial reply went unanswered. The phone was silent. Dr. Moon had hung up!
The Doctor thought about the message. Short. Minimal information. "Lower the shields" could be a trap. Pretty obvious trap though. He glanced at the console again, still no other ships around, too high for the Vashta Nerada to get off the surface - which was a pretty good place to be.
"A short, minimal information message requesting that I lower shields." The Doctor thought.
"Oh I'm daft!" The Doctor exclaimed, not even noticing no one was around to witness his post-daftness brilliance.
"Dr. Moon didn't want me to lower the shields so that we could talk directly, he's software! Over the phone is as directly as he gets! That was the message. Someone else gave him the message!" The Doctor monologued while excitedly flipping switches. "And if I'm right, and I am usually right, that" [button, button, switch] "someone" [string of five switches] "is" [big lever] "River!"
The TARDIS control room lights dimmed a bit and its hum changed key as the shields went down, then a moment later it all came back with the console blinking wildly on every indicator.
"No!" The Doctor exclaimed as he watched the console flash in front of him. "Don't reconfigure that!" He reached out but the console burst sparks from just under his hand and he pulled it back. He ran around to the other side. "Oh, that, is going to take weeks to set back right." He held out his hand hesitating to try the console again when it stopped.
He heard a shimmering electronic whisper behind him and turned around just in time to see Dr. River Song finish transmatting in.
"Hello Sweetie." River grinned.
"River!" The Doctor ran to her, "How?", holding her, an inch away.
"Oh shut up and kiss me."
She got her way. (She usually does.)
"I like the new face. I always did have a thing for older men."
The Doctor catches his breath and composure, and began again. "One. You were dead."
"I got better."
"Two. You can't transmat into the TARDIS."
"She likes me. And I did a bit of reprogramming on that. Oh, which reminds me, your shields are down." River presses two buttons and flips a switch, listens to the hum of the TARDIS change key back to normal. "That's better. Also…" River taps a few keys, reads a screen on the console, taps a few more keys to clear it.
"What were you checking just then?"
"Spoilers."
"It's alright. I figured it out. Later you, you on this timeline, sends a message back in time to me to bring me here and now, and also a message just now by way of Dr Moon. You had to send a minimal message through Dr Moon so that it wouldn't pollute the timeline. Well. It worked, you're brilliant."
River just smiled.