This is a rather rushed description of Silence in the Library and Forest of the Dead because it focuses more on the Doctor and Rivers emotions than on the actual episodes. Now that we know that River Song is the Doctor's wife, Amy and Rory's daughter and part Time Lady her death seems even more tragic.
The First and the Last
When the Doctor and Donna arrived in the Library the Doctor expected it to be packed with people. When he and his companion found the place empty yet with life signs all over the planet the Time Lord began to get worried. Then the rocket arrived and out stepped a woman whom the Doctor had never seen in all ten of his lives.
"Hello Sweetie," said the woman with an affectionate smile. The Doctor was caught off guard by her words but quickly recovered.
"Get out," he said and then spoke to her companions warning them all to leave. They all ignored him and the woman who had called him Sweetie took off her helmet revealing long curly blonde hair. The Doctor assumed she was a flirt and that she probably said sweetie to everyone. He was wrong.
The woman introduced herself as Professor River Song. This name meant nothing to the Doctor though he admitted that he liked it before trying to steer her back to her ship. River and her companions refused to leave. River quickly relieved the Doctor of command which surprised the Time Lord and also made him uncomfortable. Ever since he'd regenerated into his tenth incarnation – and for several incarnations before that – he had always been the one to take the lead. She ordered him to join her at a desk but he assumed she was speaking to someone else when she said "Pretty Boy".
"Pretty Boy, get over here!" she called again and the Doctor looked up to see her glaring at him.
"Oh I'm pretty boy?" he said.
"Yes," hissed Donna and nodded towards River. The Doctor went to join the curly haired woman who took out a small book that looked remarkably similar to his TARDIS.
"Thanks," River said.
"For what?" said the Doctor.
"The usual," River said. "For coming, when I called."
"Oh that was you?"
"You're doing a very good job of pretending you don't know me," she commented, "I assume there's a reason."
"A very good one actually," the Doctor said. River flicked through her book.
"Right," she said, "Let's do diaries." She looked at him, "Judging by your face I'd say this is early days for you." She spoke of a few events that meant nothing to the Doctor. He simply stared at her blankly. River stopped and examined him again.
"Look at you." she said softly, "You're young."
"I'm really not," the Doctor said.
"But you are," River insisted, "younger than I've ever seen you."
"You've seen me before?" the Doctor said curiously. For the first time River's cheerful and affectionate facade fell away. She stared at him with an almost pleading expression.
"Doctor," she said quietly, "Please tell me you know who I am." The Doctor looked at her, then at the TARDIS shaped diary before staring at her again.
"Who are you?" he asked.
Those three simple words tore River apart. The Doctor had said them before but she realised that this time he really didn't have a clue. She'd known from the moment she first saw him in this incarnation that he didn't recognise her but she'd desperately attempted to find some trace of her Doctor within this stranger.
River stared at the man she loved. He wasn't the same person she had known for her whole life. That was to be expected; regeneration affected a Time Lords personality in addition to their appearance but the Doctor had known her since she was a baby, even while she was being raised to murder him.
River was distracted from her heartbreak by a scream. She, the Doctor, Donna and the other people that had arrived in the ship sprinted towards the sound. They were too late. All that was left of Miss Evangelista, who'd been a brief but close friend of River's, was a skeleton.
Furious and devastated River growled, "Whatever killed her, I'd like a word with that!"
"I'll introduce you," the Doctor said grimly.
The creatures that had killed Miss Evangelista where known as the Vashta Nerada. River had never heard of them and she was an experienced woman but according to the Doctor many planets, including earth, were infested with these creatures. It reminded her that, although she was part Time Lady, her lifespan was still considerably shorter than the Doctor's. That made her feel sad but she hid it as she always did behind a feisty and cheeky exterior.
As their adventure continued the Doctor grew more hostile and after Donna disappeared and the Vashta Nerada killed several of their companions, River grew frustrated with the Time Lord. They got into an argument and Mr Lux, the leader of the archeological team, lost his temper.
"Oh for heavens sake!" he roared, "We're all going to die here right now and you two are squabbling like an old married couple!" River looked at him for a moment. What Lux didn't know was that she and the Doctor actually were a married couple and although she was centuries younger than the Doctor, River was still older than a human due to the fact that she was part Time Lady. She turned back to the man who would become her husband and decided it was time to tell him a secret that could not fail to gain his trust.
"Doctor," she said, "Someday I am going to be someone that you trust completely. But I can't wait for you to find that out, so I'm going to prove it to you. And I'm sorry. I'm really, very sorry." She leaned up and whispered into his ear...
River Song intrigued the Doctor. She seemed to know him very well but her knowledge of him made him feel uncomfortable. He was suspicious of how she had learned so much about him. Throughout their adventure in the Library, River kept revealing more surprises such as the fact that she possessed a sonic screwdriver which she claimed he had given to her. However nothing could have prepared the Doctor for the secret that she whispered in his ear.
The Doctor froze in shock and stared at her as she pulled away from him. The Doctor was almost never speechless but River's secret had caused his vocal cords to stop working. He couldn't do anything except stare at her.
"Are we good?" she asked. The Doctor tried to speak but couldn't, "Doctor are we good?"
"Yeah," the Doctor croaked and River let out a breath that she'd been holding.
"Good," she said.
This adventure had been a nightmare for River. Not only had she lost several of her friends but the love of her life didn't know her. However realising that she had finally earned his trust made her feel a little better and helped block out some of the grief that was threatening to consume her. This was her last meeting with the Doctor and she was going to savour every second of it. Pushing back her emotions she regained her composure and she, the Doctor and the only other survivor of the Archaeological team, Mr Lux, went to find CAL who, to River and the Doctor's shock, was a little girl wired into the main computer. Lux explained that Charlotte Abigail Lux had been dying so she'd been brought here where she could entertain herself for eternity with every book ever written.
As always the Doctor was willing to sacrifice himself for the greater good. In order to release the people who were saved within CAL – one of which was Donna – someone had to die. River was not going to let the Doctor sacrifice himself. She'd never allowed him to do it before and she wasn't going to now, even if it was a different Doctor from the one she knew. If he died then she would never have been born but River wasn't thinking about that; all she was thinking about was saving the man she loved.
River had always had a bit of an interest in bondage and took handcuffs with her wherever she went; her interest had been developed through her time in prison. She knocked out the Doctor and handcuffed him to a pipe, just out of reach of her diary and his sonic screwdriver. To her relief the Doctor woke up before the countdown was finished; she didn't want to die without saying goodbye.
When the Doctor woke he remembered, with a sense of outrage, that River had punched him! Outrage was quickly replaced by confusion when he realised that he'd been handcuffed to a pipe. And confusion was replaced by horror and desperation when he realised what River was going to do.
"No, no, no!" he cried, "What are you doing? That's my job!"
"Well I'm not meant to have a career I suppose," River said calmly. The Doctor looked at his cuffs then back at River.
"Why do you even have handcuffs?" he asked and River smirked.
"Spoilers," she said.
"This is not a joke!" roared the Doctor, "This will kill you! I have a chance! You don't have any!"
"You wouldn't have a chance and neither do I!" River yelled at him and for the first time the Doctor realised that she was scared. "I'm timing it for the end of the countdown," she said her fear quickly replaced by the calm demeanour she'd had a moment ago, "That will increase our chances of a clean download."
"River please no," the Doctor begged.
"Funny thing is," River said in an almost conversational tone; her voice was trembling slightly which once again told the Doctor that she wasn't as calm as she was pretending to be, "this means you've always known how I was going to die. All that time we spent together you knew I was coming here. The last time I saw you, the real you, the future you I mean, you turned up on my doorstep with a new haircut and a suit." She was losing her composure and both of them knew it but she still pressed on, "You took me to Darillium to see the Singing Towers." She sighed and for a moment a tiny smile flickered across her face, "What a night that was. The Towers sang. And you cried. You wouldn't tell me why but I suppose you knew it was time; my time; time to come to the Library. You even gave me your screwdriver. That should have been a clue." The Doctor reached desperately for his screwdriver; if he could just reach it he could stop River from going through with this suicidal act. "There's nothing you can do," River said gently.
"Let me do this!" the Doctor yelled in desperation.
"If you die here it'll mean I never met you!" River snapped.
"Time can be rewritten," the Doctor said.
"Not those times," River said and the Doctor saw that she was close to crying, "Not one line. Don't you dare?" The Doctor stared at her helplessly, "It's okay. 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." The Doctor watched as she started crying.
"River you know my name," he said unsure of where he was going with this but knowing that her knowledge of his name was one of the most important things in the Universe, "You whispered my name in my ear," River smiled sadly at him, "There's only one reason that I'd ever tell anyone my name. There's only one time I could."
"Hush now," River said and the Doctor glanced at the clock; only four seconds left. River smiled the affectionate and, the Doctor now realised, loving smile that she'd shown him when she first arrived, "Spoilers..."
With that last word, River Song downloaded the people trapped in the library. There was a massive flash of light and the Doctor turned away. When he looked back, River Song was no more.
The Doctor sat there for a long time staring at River's corpse. She had died for him. It wasn't the first time someone had died for him and he doubted it would be the last but somehow her death affected him more than most of the deaths he had watched throughout his ten lives. He barely knew her yet he knew with complete certainty that he had just lost someone who would be very special to him in the future. The fact that he was going to see her again made him feel a little better but he still felt as though he had lost a dear friend or maybe even more. The way she'd acted around him told him that their relationship would become much deeper than friendship. That must be why he felt almost as miserable as he had when he'd placed the Time Lock on the Time War.
When Donna found the Doctor she found him handcuffed to a pipe staring into space.
"Who handcuffed you?" she said and the Doctor jumped slightly and turned. He relaxed when he saw it was her and gave a small smile.
"River seems to have had an interest in bondage," he said.
"Oh my god," Donna said staring at River's body, "She's..."
"She sacrificed herself to get you out of the computer," the Doctor explained, "Pass me my sonic screwdriver will you?" Donna passed it. If she didn't know the Doctor so well she'd think that River's death hadn't affected him at all but she could see in his eyes that River's death had actually affected him very deeply. And he barely even knew her.
The Doctor jumped upright as soon as he'd used his screwdriver to unlock his cuffs. He moved with as much agility as ever but Donna noticed that the manic enthusiasm he normally possessed had diminished. He looked at the handcuffs for a moment then tucked them in his pocket.
"Looks like you've got an interest in bondage too," Donna teased. The Doctor looked at her and Donna saw in his expression that the handcuffs were not something he was taking for pleasure. Instead they were a memento of his time with River. She quickly went silent, realising that her little joke had not made the Doctor feel any better.
"Come on," the Doctor said, picking up River's diary and screwdriver. The two of them left the room.
The Doctor and Donna were preparing to leave when the Doctor suddenly had a thought. He had left River's diary and screwdriver on a ledge but sprinted back towards them and grabbed the screwdriver.
"I gave her my screwdriver," he said, "Why would I do that? All those years we spent together I could think of a way to save her. Future me gives her my screwdriver. Why would I do that?" Then he saw it. A tiny panel that all of River's archaeological team had built into their suits which allowed their consciousness to survive for a short time after they physically died, "Oh, look at that. I'm very good!"
"What have you done?" Donna asked. The Doctor held up the screwdriver and showed her the panel.
"Saved her," he said and then he ran.
The Doctor could not remember the last time he'd run so fast. Adrenaline pumped through his body as he dodged around shelves, leapt over chairs and desks and slammed his way through doors as he headed towards the main computer. He'd run for his life more times than he could count but this was different. Now he was running with all the speed he possessed to save the life of a woman whom he barely knew and was already dead. However this was not just any woman; this woman knew his true name, something that he'd never told even his closest companions.
"Stay with me!" he bellowed encouragement to the screwdriver, yelling at River to hang on, "You can do this; stay with me! Come on! You and me, one last run!"
He burst into the room where the main computer had been built. CAL smiled at him as she realised what he was doing and he grinned back as he jammed the screwdriver into the computer. If he'd been just a few seconds later he would have lost her but he'd reached CAL just in time. He sighed with relief as he safely uploaded River's consciousness into the computer. Exhausted but pleased the Doctor stepped back and looked up at the data core imagining River alive and well inside it.
Inside the computer River was reunited with her dead archeological team and became the adopted mother of CAL and two virtual children. CAL said that the Doctor had fixed the computer and that it was safe and good now. But River still did not feel entirely happy. The Doctor had saved her just as he had done many times in the past (or the future from his point of veiw), but now she was separated from him and it was not the same as the frequent separations they'd had in the real Universe. He was alive and no doubt saving the Universe and maybe other Universes too, while she was, to put it simply, dead. However River knew what the Doctor was capable of and if there was any possible way for them to be reunited then he would find it. River clung to that hope as she stood outside the children's room, holding her TARDIS diary.
"I will wait for you my love," River said softly.