Sometimes there are miracles
As Clara lay gasping for breath on the TARDIS floor, the Doctor stood over the other girl, the one she brought back. The Doctor had just fished them out of his time stream, and neither of them was in good shape. Clara tried to get up, but the Doctor instead picked her up and carried her to bed, saying she needed sleep. The other one, however, looked like she might not wake for a while.
He didn't know how she'd got there, and he didn't like not knowing. He decided that the best bet would be to run tests on both girls, just to make sure they were safe.
As he dragged the young girl to the medical bay he got a terrible head ache. Being so close to his time stream was sickening. He placed the girl on the examination table and began scanning. What he found was impossible. The adolescent's biological makeup was shifting, as if she were going through a chameleon arc. Slowly but surely, most of her DNA was becoming Gallifreyan.
Already a lump was forming on the right side of her chest, a lump the Doctor was sure would be a heart. The Doctor understood what was going on, but not why. He also understood why she hadn't awoken. She was changing species.
Though, he noticed, not all of her. Her personality, the way she thought, the deepest most center part of her being was remaining human. She would be a Timelord, but not 100 percent.
He picked up the girl, who he saw couldn't be more than 13, and took her to the room the TARDIS had prepared for her. He placed her carefully in bed, and went back to Clara.
She was awake, but just barely. He took her to the examination table and scanned her too. He was absolutely giddy when he found the same results. He smiled when he discovered the truth: he was no longer the last Timelord. More than that though, he realized something even better. He could be with Clara.
He decided to celebrate by doing the drunk giraffe. He had just started his terrible dance when Clara sat up, panting and wheezing. Quickly it became panting, wheezing, and laughing. "Nice moves, Chin Boy," she said once she could talk again. The Doctor grinned and ran over to tell her the news.
He never got to. Just before he got to the table, Clara started to glow. Her smile swiftly faded as she saw what was going on. They both heard a loud scream coming from the girl's room. "Lili-ahhhhhh!" she started to say, but was cut off by a gut wrenching cry of her own.
The Doctor ran back, trying not to get by regeneration energy. He ran behind the control console, but was grazed by the golden light on his left arm. He ignored it for the moment, and waited. "It must be complete," he muttered, "This must be the last step." Just then the girl's shout ended, and a bit after that so did Clara's.
"Doctor! Doctor, what's wrong with my voice?" he heard her call. This new voice of hers was lower and, errrrrm, bittersweet? Yes, that was the word. The Doctor liked it. A lot. Slowly he peeked around the corner of the flight console to look at her. What he saw took his breath away. She was tall and lean, with black hair that tumbled down her back in waves. She was tan, with full, red lips. But it was the eyes that did it for him. They didn't stay a certain color, but looked like a kaleidoscope, shifting and changing from deep brown to clear blue to soft green. He took one look at them and was done.
"Doctor! Come here, Chin Boy, or I will smack you so hard…" she yelled at him, but in this form it sounded more like a flirt than a threat. None the less, he crawled out of his of hiding place. Clara stood up, and suddenly looked aware that something was different. She used to be a full head shorter than him, but now the Doctor saw she could look him straight in the eye. He liked this too. It'd be easier to kiss her like this.
"Doctor, what's wrong with me? What happened? Last thing I remember is you doing a terrible dance and then there was a light. Why do I sound different?" she asked looking nervous. The Doctor kissed her on the forehead and was about to explain when the other girl ran in, now sporting a completely new face.
The child had been small with long blonde hair and pale, blue eyes. Now she was tall and thicker, with a golden brown pixie cut and emerald eyes that glowed with excitement. The girl had a line of freckles down her nose and a smirk that said that you shouldn't trust her with fire or sharp objects.
"Wow, you look good," she said, glancing at her. "Now, more important business: how do I look? I know I'm taller and my hair's short, and -Hey! I'm American! - but tell me honestly. Am I still gorgeous?" she asked, batting her eyes.
Clara inhaled. "Lilia? Lil, is that you?" she gasped. The girl whose name was apparently Lilia winked. "Yup! I'm the new and improved, regenerated Timelord style, completely fabulous Lilia 2.0!" she sang. She ran around the console, did a front flip down to the medical bay, and landed in a curtsey while doing jazz hands.
Clara looked in shock and the Doctor smiled. "I like Lilia," he started, "Lilia is cool." Clara laughed at this, a beautiful sound like silver Christmas bells. "Okay, okay…? Doctor, for the last time, what happened to me and Lilia?" she said in her teacher voice. The Doctor swallowed, suddenly completely nervous.
"Ummmm, actually, it seems that you and Lilia have," he paused and dropped his voice to a barely audible whisper, "become Timelords." Clara gave him a look that would've scared Amy Pond.
"What?! We've become what?!" she asked, lowering her voice to a growl and doing a slybrow. The Doctor wished he could slybrow, but unfortunately he hand a seeming lack of eyebrows. He shook his head to get back on track and gave Clara a look that said 'Please, please, please don't kill me!'
` "Well do to micro-engineering and biology re-authorship that seem to have taken place as a result o-" he started when Lilia slapped him across the face. "In English, please so we can understand it," she said, giving him her sweetest smile.
The Doctor gulped and looked at the ceiling. "You and Lilia have somehow, someway become Timelords. Not fully, but close. According to the scans, you have all the physical Timelord attributes like long memory, heightened senses, and regeneration, but your mind is still human. You have human emotions and personalities in Timelord bodies!" he said, practically screaming with joy at the last bit.
He noticed though, that Clara was less enthusiastic. She was pacing back and forth, running her hands through her brand new hair. "If we regenerated, why am I still the same? I mean, I still like these clothes and I still want to bake soufflés and I'm still me. From what you told me about the whole process, I should be entirely different," she said. The Doctor rolled his eyes and grinned. "That's the human bit of it! You have the same personality because deep down inside, you guys are still human!" he said, and started dancing again. "Oh no! Not that! Anything but that!" Lilia cried, covering her eyes to block out the horribleness of the drunk giraffe.
The Doctor stopped dancing. He just realized something. No matter how cool Lilia was, he had no idea who she was. For all he knew, she could be a really clever Zygon. "Who are you and how on Gallifrey did you get in this ship?" he asked, glowering at the playful brunette. Lilia stepped back and Clara stepped forward.
"She is Lilia Annabeth Oswin, and in one of those other lives she is our daughter," Clara said, pulling herself up to her new height.
The Doctor fell back into the chair by the console, rubbing his temples as he was pulled back into a memory. He was in his 10th incarnation, and just before he regenerated he met a woman in 22nd century London. She was beautiful and kind, and in a moment of weakness he slept with her. It was wonderful and amazing, but a voice in the back of his head said 'No, not yet. Wait wait wait.' so he left the next day. He went to Elizabethan England, but he couldn't remember what he did there. Later he went back to visit the lady he had one good night with. He was confronted by a child who claimed to be his and the death of the girl who he barely knew. He now recalled her name. "Clara Oswin," he muttered, and started to cry.