This is a theory presented by Professor Evans, so I give all credit to her and thank her for letting me write this, because I think it's a really awesome idea. Her theory, my plot. Spoilers for The Sarah Jane Adventures episodes "Death of the Doctor" Parts 1 and 2.
Disclaimer: Neither Professor Evans nor I own Doctor Who. However, we do occasionally pretend to be Time Lords.
The Doctor woke from his drug induced state, slowly becoming aware of his surroundings and disliking them very much indeed. His arms and legs were strapped down to the bed beneath him and he was slowly being transferred to an upright position, noting that the bed itself was indeed moving. There was a solution being delivered intravenously into his arm, which he had to admit was rather uncomfortable. His vision began to clear and he blinked several times in quick succession.
The room in which he was being held was sparse, with only the bed beneath him, a table, and a few large pieces of equipment. The black console not far from him seemed a bit familiar, but he couldn't quite place it. The ceiling was spinning in every possible direction.
He tested out his mouth; it was dry and very much in need of a drink. He then attempted to clear his throat, but failed miserably. His raspy voice was barely audible as he weakly pulled against the straps. "Amy? Rory? Where are you?" They had been... Somewhere. On a planet that wasn't Earth, when they'd been... knocked out and kidnapped?
"Your companions are in their holding cells, Doctor."
The Doctor quickly turned his head to the right, taking in the sight of a giant... vulture.
"The Claw Shansheeth? You again?"
"Of the 15th Funeral Fleet," the creature said, rather proudly. "I am one of the few left from your last... Encounter."
"Sarah Jane and Jo turned them all into chicken wings," he declared dizzily. The Claw Shansheeth had faked the Doctor's death in order to draw out Sarah Jane and Jo Grant, using their memories of their time with the Doctor to create a TARDIS key with a machine called a Memory Weave, which turned memories into physical objects. It was rather complicated. The Doctor peered into the bag that was feeding him liquid. "I don't suppose this is what's keeping me weak, is it?"
The vulture-man made a noise that sounded like a condescending snort. "I still need you alive, Doctor. It will not kill you."
"What is it?" he demanded harshly. It could be killing him.
"All in good time." The Shansheeth crossed to the console, black robe swaying to and fro as he walked.
The movement made the Doctor dizzy and he shook his head to clear it. Only then did he realize there were probes of some sort stuck to his head. "What are these for? You aren't making a TARDIS key from me!"
"I don't have to," the Shansheeth replied. Its beak clicked together and the Doctor got the distinct impression that, had it possessed a mammalian mouth, it would be smiling. "Your two human companions were incompatible. The woman's brain almost destroyed my machine."
The Doctor smiled lazily. "Little Amelia Pond, with the Universe running through her head..."
"What I will get from you, Doctor, is worth far more than just a TARDIS key. I will use your memories against you and they will open doors to the future! We can prevent deaths all over the universe!" The bird began pressing buttons and the device powered up, a noise that suddenly jolted the Doctor back to reality. He quickly crossed the room and removed the needle from the Doctor's arm, wheeling the drug away.
"No, no! What are you doing?" The Doctor squirmed weakly against the bonds, but they held fast. His eyes darted quickly around the room. The table to his left contained every item from the pockets of his tweed jacket, sonic screwdriver included. The electrodes on his face suddenly became warm. His eyes went wide and he stared at the giant vulture creature, once again behind the console. "You can't stop things that must happen!"
"Those events are for me to decide now, Doctor!" The creature lifted a lever and the Doctor felt a jolt of electricity flow into his head. He clenched his teeth, determined not to listen to anything the Shansheeth said. What the vulture did say, however, was the last thing that he would have expected.
"Doctor, think of your companions."
"Think of my companions?" Brilliant Amy and Rory. Who knows where they are right now? Afraid, perhaps. They have each other, of course. Amy is probably trying to break the bars of the cell with Rory attempting to help and being completely rubbish at it- "hold on, why is he telling me to think of my companions?"
"What are you trying to do?" the Doctor demanded, as the Shansheeth increased the voltage.
"I will have a companion from this machine, Doctor. A companion made of your memories, one who will be able to infiltrate your TARDIS and fly it to the satisfaction of the Shansheeth!"
"What?" How could the Memory Weave create living beings? That was probably a question for another time. The Doctor tried to think of anything else, anything but Rory and Amy, but it was so difficult. He was worried about them, where they were, if they were hurt. The nodes on his head were hot now and the electricity was steadily increasing. Two of his friends were currently prisoners of a vulture! It was impossible not to think of at least ONE of his companions-
"That's it! If I can't NOT think of a companion, I'll just think of them all!"
His mind began to overflow with thoughts of every previous companion, even those who were fleeting and rare. Ian, Barbara, his dear Susan, Turlough, Jamie, Liz, Jo, Sarah Jane, Romana, Tegan, Nyssa, Adric, Peri, Ace, Mickey, Captain Jack, Martha, Donna, Amy, Rory. All those and so many more people who had accompanied him on his journeys flashed through his mind. He refused to let the Shansheeth have even a single one of them.
The console beneath the vulture's hand sparked and he let out a flurry of colorful curses. "You will not best me, Doctor! You cannot overload this machine!"
"Try me!" The Time Lord boasted, letting more and more memories flood his mind. He had forgotten just how happy these memories made him, even though they often ended in tears.
The console sparked and shuddered, making a labored whirring sound. The vulture cursed again, trying and failing to keep the machine from overloading. "I will have my prize!"
"Not if I can help it!" The Doctor shouted. His strength was slowly returning. Soon he would be out of these bonds and rescuing Amy and Rory.
The machine suddenly doubled the amount of electricity, causing the Doctor's head to arch back in pain. He screamed.
"Give me the companion!" The vulture screeched. A faint wisp of golden light drifted from the Doctor's forehead. "Yes! It's working! Give me my companion, Doctor!"
The Doctor tried to focus, but it was becoming harder and harder to clearly differentiate between each friend in his mind. The golden light began to glow and he lowered his head to his chest, fighting against the harsh power that was running through his body. The light took form and a golden mist drifted just above the surface of the floor. The electricity increased even further and he felt darkness prick at the corners of his eyes. "I can't let him win, can't can't can't..."
The longer the exchange went on, the brighter the light became. The Doctor was on the very edge of passing out at the golden mist began taking the shape of a humanoid. "Please, no!"
The Shansheeth increased the voltage a final time and the Doctor promptly passed out.
Several minutes passed before the Doctor regained any semblance of consciousness. He had the worst headache he could ever remember having. His brain felt like mush. Brilliant mush, but mush nevertheless.
He reached up and rubbed his eyes. He immediately took his hands away and blinked. "My wrists are free..." He also made a mental note that the bed beneath him was now lying flat instead of propped up as it was before. His head was so dizzy, but he managed to sit up without too much trouble. An acrid smell reached his nose and he wrinkled his face in disgust, standing carefully from the bed, pleased to discover that his legs were in decent working order. "But where is the..."
His train of thought immediately became derailed as his eyes caught a bit of black robe poking out from the side of the console. He rushed over to find the Shansheeth dead, the needle from the intravenous drip stabbed neatly into its forehead. He gaped, speaking half to himself and half to the air. "What happened to you?"
He immediately turned, albeit a bit dizzily, and caught sight of another person in the room, sitting huddled in the far corner. Legs were drawn up to hide the form beneath, but he would have recognized her voice anywhere. The bed that he had been strapped to somewhat obscured her figure, but he walked around it, observing her as carefully as he could. This was... impossible.
"You know," she said casually. "It would be awfully nice if I could get some clothes. I'm rather exposed."
He completely ignored her, staring in continued disbelief. "How did you get here?"
"No offense, but I'd like some clothes before I answer your inevitable plethora of questions."
"This is completely impossible, how did you-"
"I'm naked," she pressed, more firmly this time.
The Doctor paused, as if suddenly realizing this very thing. "Oh. OH. Yes, um, right. Let me get you something out of the TARDIS. I'll be right back!" She shook her head as he ran out the door.
The Doctor, after making three wrong turns and blaming the TARDIS for bad directions, finally arrived at the police box. He rushed inside and bolted for the wardrobe, finding that an outfit was already hung out for her. He shook his finger at the ceiling. "Just because you like her doesn't mean she gets special treatment!" He grabbed the outfit and carefully made his way back to the woman, who was still huddled in the corner.
She seemed pleased with the clothing choice and carefully took the outfit from him. It took him several seconds to realize that she wanted him to turn around while she dressed. "Well how was I supposed to know?" he said, defending himself as she quickly slipped the clothing on.
"Do you usually watch females dress?"
"No, but- Oh, shut up." He waited until she gave him the okay, then turned around again.
She shushed him before he had any time to speak. "I don't know where I came from and I don't know how I got here, since I know you were going to ask."
"But you... I didn't even think of..." The Doctor began pacing about, speaking aloud to himself. He picked up his sonic screwdriver along the way, paused to scan her, then continued the pacing. "So I tried to overload the Shansheeth's machine by thinking of multiple people instead of just Amy or Rory or-" He froze, then spun on his heel to face her. She didn't look scared, not exactly. Just slightly apprehensive under his bright eyes.
"You don't know me," he said. It was a statement, not a question. "This is the first time you've ever met me... That machine didn't make a single companion it made... all of them. All of them into one person." He scanned her again, to make sure. "Human," he confirmed.
"You've met me before?" she asked, surprised. Her curly hair bounced whenever she moved her head. He wanted to pull on it and watch it spring back, but he restrained himself.
"Many times," he replied softly. He slowly put the sonic screwdriver back in his pocket. "Oh this is... I don't even know what this is," he admitted, running a hand down his face.
"That sounds encouraging," she replied, a bit testily.
Suddenly his arms were around her in a hug, comforting and warm. She blinked. "Uh, Doctor?"
"Oh, you do know my name! That spares that part of the introduction!" He couldn't help smiling as he squeezed her tight, then let go. "We have so many things to do!"
"We?" she asked, confused. She trusted this man implicitly, though she wasn't sure why. He seemed to know where she came from, in the least. And though she had no previous memories of her own, she knew many, many things.
"You're coming with me, of course," he declared. "As soon as we rescue the other two."
She paused in thought, then shrugged. "Works for me."
He smiled, eyes bright. "So, what is your name?"
"I thought you knew my name?" she asked, eying the items on the table behind him as he unceremoniously stuffed them all back in his pockets at once.
"What's the fun in that?" he replied, rediscovering a pair of gloves that he had been particularly fond of a long time ago. He turned to her expectantly. So many things made sense now. He wasn't sure just how much of his knowledge was in her head and what things he would have to teach her. Teaching had never been a problem, though.
He loved her already.
"Hm. I don't know. What do you think my name should be?" she asked, honestly interested in his opinion. She knew him, but she didn't know him. But according to him, she would some day.
She was new. The woman she would become was important, a woman who possessed adoration for him down to her very DNA. And now he realized just what impact this would have on everything. He knew now why the future him loved her so much. It was because she was them. "What about River Song?"
She paused, then smiled. "River Song. I like that name. River Song it is, then!"
He smiled and grabbed her hand, pulling her along as they raced off into the bowels of the Shansheeth cruiser, searching for Mr. And Mrs. Pond.