The Doctor lay on the floor, gasping, listening to the sounds of the TARDIS as she hummed and flew through time and space. He had just let Amy and Rory off back on Earth; they had wanted some alone time for a few months. And as the Doctor had been walking back to the TARDIS in the streets, a simple mugger had attacked him. The Doctor who could fight off Daleks, weeping angels, and all sorts of other insanely powerful creatures, yet it was a simple, weak human who had hurt him.
And unfortunately, these wounds were killing him. The Doctor had managed to drag himself back to the TARDIS, where "she" had automatically opened the door for him, probably somehow sensing his pain. The inevitable was coming; the Doctor would have to regenerate, and turn into his twelfth incarnation.
He chuckled to himself as the TARDIS continued to hum, carrying him away to nowhere in particular; maybe he would turn into a ginger. Another part of him was sad though; he liked eating fish fingers with custard, saying "Geronimo", wearing bowties and the occasional fez… Even though he would remember these things, and having liked them, didn't mean that they would necessarily remain the same. But hey, he could still potentially still like all of those things after regenerating. After all, both his ninth and tenth incarnations had liked bananas. Certainly the Doctor would still like some of the same things in his twelfth incarnation!
A searing, burning hot sensation shot through his body; the reincarnation process had officially begun. It was too late. The faint glowing had started, and at the peak of the cycle, it would erupt into light all around him. The Doctor dragged himself over to the control console, and pulled a lever. He wanted to land on a planet and get outside of the TARDIS before that part of the process occurred, otherwise the TARDIS would experience quite a deal of damage as she had done when he had last transformed.
The TARDIS landed on some uninhabited planet, but that didn't really matter to the Doctor at that moment. He just had to get outside. Obligingly, the TARDIS opened the door for him as he staggered to his feet, blood staining his shirt. He patted the doorframe as he stumbled out.
"I won't be long, you sexy thing. I just can't have you getting wrecked again like last time, eh?"
The Doctor managed to stagger about another twenty yards before he finally collapsed to the ground. The light was growing brighter, and the moment had finally come. He shut his eyes as the light, as HE exploded, his body morphing and twisting into a new individual. In his minds eye, he thought of all the companions he'd ever had, and if Rory and Amy would still travel with him, if River would still love him in a new form.
Finally, the pain stopped, and the heat faded away. The Doctor sat up, curly gold locks of hair cascading down his back. He inspected his hands; they were smaller and daintier. And for some reason his clothes were much larger on him than before, and there were lumps under the shirt. The Doctor stood to walk to the TARDIS, when his shoes fell straight off; they were too big. The Doctor began to fear what all of this meant, and ran into the TARDIS on the border of hysteria.
The Doctor grabbed a mirror, and stared into it. The eyes were definitely still the same, and the prominent cheekbones were still there, but the lips were red, and the eyelashes were long and thick, and he was most definitely a GIRL. He was now a she.
The Doctor screamed. Far away, Amy Pond felt a shiver run down her back.