A/N — First off, whilst personally, I would view this as a fix-it, fair warning, no one is getting saved from the Library mainframe in this.
There are a couple of reasons I went this route, firstly River being rescued has been done by a lot of people in various wonderful, beautifully written and clever ways that I can't hope to live up to. Secondly, considering the Doctor cried at Darillium and Steven Moffat said in interview (although I can't find it now) that the Library is the happiest ending she's going to get, I think this is plausible.
The End of All Things
He walked against the flow of people gradually milling towards the transporters. No one seemed to take notice of the man in the morning suit doing the opposite of what they were all doing — the man going deeper into the library. He kept his head down and carried on until the flow of bodies became a trickle and he finally arrived in a part of the library where there was no one. No one living at least.
He closed his eyes and steadied himself before turning the corner to where he knew he would find her. There in the centre of the room, covered in a blanket was River, just as he had left her hundreds of years earlier, or an hour ago. His throat closed up and he gasped for air; a terrible sob penetrated the silence.
He compelled his legs to approach her. The truce with the Vashta Nerada was going to end soon and he had no more time to waste. His shoulders hunched and his body convulsed as he neared her still form. The surge that had flowed through her had destroyed her hearts and brain, but outwardly she looked unharmed, almost as though she were sleeping. Almost.
He placed a trembling palm to her cheek; it wasn't yet cold but there was no movement at all, no neurons firing, no hearts beating. This was a shell.
The anguish tore through him and he pulled her body up, pressing it to his; her arms hung limply to the ground. He shuddered as he rocked her, spilling tears all over her face and neck. He wanted to lie down with her and wait for the Vashta Nerada to come and strip the flesh from his bones until he was gone too, but he still had more to do.
He eased her gently back down onto the floor, cradling her head, and adjusted the blanket around her. Angora, she was allergic; he hadn't known when he first wrapped her in it, and it didn't matter now.
At the time he had been more distressed by how much it upset Donna, who insisted on helping carry her body up from the core, than the fact that he was holding the dead body of his future wife in his arms. Or perhaps that was the easier pain to focus on, rather than the soft edged pang of pre-emptive grief.
If it had been soft then, it was sharp now as it clawed its way out through his sternum and spine. He opened his mouth to tell her he was sorry. For the angora and for not knowing, and for everything else she had suffered because of him, but he couldn't make a sound.
He moved to the terminal, rubbing his eyes roughly with the heels of his hands so he could see, and attached a signal booster to the casing. He took a timer from his pocket, set it next to the screen and began typing commands.
River was curled up on the settee watching a film, when the picture began to fizz and stutter. Her stomach flipped and she sat bolt upright as the Doctor's face — her Doctor's face — come into view. She hopped from her seat and sank down in front of the screen.
"At last. I was beginning to give up on you, you know?" She laughed, relieved. "I have absolutely no sense of time; it's driving me mad. It feels like I've been in here forever and no time at all. How long has it been out there?"
"About half an hour," he replied, the tone of his voice telling its own tale.
"You're crying. You've just come from Darillium, haven't you?"
"Yes," he said, straining to contain the emotion.
She wanted to reach through the screen and hold him and tell him that it would be okay, that she was here now, but somehow she just knew.
He had no plan.
Tears burned at the back of her eyes. The virtual world was so painfully close to living that it made the fact that it wasn't even harder to take.
"I tried everything; I…I couldn't find a way."
"Why then? Why did you put me in here if you knew you wouldn't be able to get me out?" she demanded, her sorrow infused with anger now.
"River, the first time I met you, you saved my life. In so many ways. You made me promise not to change anything. If I thought there was no way of saving you, I don't think I could have kept it. Seeing you die with no hope— I couldn't have kept fighting all those years."
River's hearts sank and she put her hand to the screen — the closest she was ever going to get to touching him again — and let the tears stream down over her cheeks. She understood. The first time he met her, she made him promise, and even though he knew nothing about her, he trusted her enough to keep it. She didn't think it was possible, but she loved him a little more for it.
"Oh, my love."
"River, I'm sorry for putting you in there. It's only half a life, but it's forever. If that's what you want."
"Half a life is no life at all," she replied.
"I can join you, when my time comes, I can programme to TARDIS to upload my consciousness—" His voice betrayed a trace of desperation.
"No Doctor." She shook her head. "This place is no more you than it is me. Besides, you'd spend the rest of your days waiting to come here. That's no way to live. You have to let me go, I was ready. I am ready."
He dropped his head and nodded; it was the answer he had expected. He knew her well enough to know that. He buried his face in his hands, weeping almost soundlessly; he knew what he would have to do and she could see that it was breaking him. "Hush," she said, "It's okay."
He rubbed his face and looked up at her, a hint of wonder in his eyes. "I'm supposed to be the one comforting you."
"We always comforted each other, why change now?"
"I wish I could hold you."
"I know, my love. If I had known that Darillium was the last chance I was going to get… I don't know. I don't know what I would have done differently." She sniffed. "I suppose I wouldn't have made that off-colour joke about flute playing chimpanzees."
He laughed through the tears, "That was funny."
"You know, I was wondering why I didn't get told off."
"There comes a time when all pretence must be dropped."
"Trust you to wait until the last minute," she said fondly. "I should really have guessed; the signs were all there. You cried for goodness sake, I could count the number of times I've seen you cry on one hand. And what led to the crying, I can count those instances on one finger."
"Here's a second finger, River. I love you." He stroked her face on the screen with the backs of his fingers. "I'm sorry if it's too little too late."
"It was never too little; I knew all along, even the version of you who uploaded me, I could see the spark ignited. At least I know now that you've always been rubbish at hiding your feelings."
He laughed again, "You always could read me."
"And you just hated that."
"Never," he lied.
"Okay, well maybe I hated it a just little bit."
"Fine, but I'm only going to let you away with that because I'm dead."
He sobbed out loud.
"I'm sorry," said River, "gallows humour. I never did know where the line was."
"It's not that. It's just hearing it said aloud. You're dead, River. You're gone. I used up all the time we had and it still wasn't enough. It could never be enough."
"No," she said, tears in her voice again. "We didn't use up time. We lived, Doctor. I lived. I made the most of every moment and I lived a long, mostly happy, life. And it was wonderful."
"It was wonderful. River Song, you were magnificent."
"The Doctor's wife."
"No," he said with a shake of his head. "You were River Song. You should look yourself up in there; see how many cultures' folklore you appear in. Fifty-eight human ones and at least twenty of those make no mention of me at all."
"Really?" she asked, with an excited wide-eyed grin.
"Go on, look it up, there's time yet."
She asked CAL to bring up all references to River Song.
Seven hundred and sixty-two results returned.
"I checked. Mostly good reviews," he said. "I can't help thinking though, if you'd been a little more gun shy your average might have been higher."
She chose to ignore the teasing and flicked through some of the legends and fairytales, smiling at the garbling of facts to fit with local custom.
"You'll never be forgotten, River. Not by history and least of all by me. You know, I never told you, but if you were to separate all of the hours I spent with all of my friends, companions and family into bundles, yours would be the largest, by some distance. I've spent the greatest fraction of my life in your company. And what spectacular company, I couldn't have asked for better."
"We had a good innings," she said, lip quirked into a half smile.
"A good run."
She could see his smile falter, almost overrun with grief, but he fought back, and flashed her a watery grin.
"Doctor, can you do something for me?"
"Leave me with my parents…my body I mean. It's what they would want."
"Of course," he said and swallowed thickly.
"Do you remember that time we went to Kulicon to bring Mum shopping for her birthday?" River asked, as much to change the subject as to reminisce. "And Dad wanted to get us a belated wedding present, but he hadn't a clue so he asked in that Ceeperian trinket shop and came out with that china tea set that turned the tea bright green?"
He chuckled, "And even though Rory told us not to drink it, we all did anyway."
"Of course we did, what's the point in making Ceeperian ceremonial tea if you're not going to drink it? Even if we were all violently ill afterward, how were we to know that it was part of the ritual to cleanse the body prior to bonding?"
"Yes, quite how the Ceeperians managed to have any birth rate at all if they were supposed to mate after that is beyond me. In retrospect, we should have looked it up before trying it."
"Or listened to Dad. He really looked after us all that week, in spite of the excessive whingeing coming from some quarters. Naming no names." She winked.
"You're a lot like him, you know?"
"If I was like him I wouldn't have drunk the tea."
"Ah but you're like your mother too, and the obstinate gene is definitely dominant. But you are like Rory; always willing to help and look after people without question, always knowing what's best for them. And that right hook of yours? Hundreds of years and a regeneration later and it still aches a bit. You get that from him too."
"The impossible Ponds, eh?"
"I couldn't have dreamt of a better family to have been part of."
"A human family. What would your old mates the Time Lords make of that?"
"They'd think it was bloody typical." He grinned.
"Nice this, isn't it? No secrets, no diaries, just talking."
He hummed thoughtfully. "Do you ever wonder how it might have gone if it could have been like this all the time? If we weren't asynchronous?"
"It would never have worked out."
"Oh come on. Before I regenerated in Berlin, and you didn't know who I was, you treated me with thinly veiled contempt. Then — bam — as soon as you saw little wifey's face, you could barely take your eyes off me. You were like a crab out of its shell: all soft and vulnerable."
"Well, it probably had a lot to do with the regenerative energy swirling out of you."
"Oh, and not the fact that you already knew what I looked like without my clothes?" She raised an eyebrow.
"Thought so." She grinned.
"In another universe there are versions of us running synchronously, and I'll wager that that Doctor loves his River just as much as I love you."
"There you go again, upping the finger count and making me cry again." She held up three fingers and he broke a little, his mouth making a sad crooked line.
"I should have said it sooner. I should have said it every day. I should have said it every time I felt it, even if that meant I was saying it all the time."
"I told you at Darillium, that you didn't need to tell me. You showed me. I knew." His timer began to beep. "What's that?"
"Vashta Nerada alarm: twenty minutes until they come looking for a meal."
"It's time," she said with quiet acceptance.
He nodded and sobbed, "Yeah."
"Don't say goodbye, I don't think—"
He looked at her and shook his head, "I won't."
He typed the command for CAL but paused his finger over the key to send it and gazed into her eyes. She steeled herself and nodded. He dropped his finger.
"I love you, River." She showed him four fingers. "I love you," he said again and she flicked her thumb out. He repeated it again and again until she ran out of fingers, dropped her hands, and smiled her last.
The Doctor turned away from the terminal, and knelt down next to River's body. He put his lips to her forehead; she was cold now. He unfastened the spacesuit and carefully freed her limbs from its embrace, leaving it a husk on the floor along with the blanket as he used the last of his energy to scoop her body up and cradle her in his arms.
The alarm increased in frequency, signalling that he had five minutes to make it back to the TARDIS.
"What do you say, River? One last run?"