Credit for the story idea goes to one of my dear fellow Whovian friends! She wrote out the plotline as a comic strip, with the cutest stick figures I've ever seen, and whatever I write that wasn't in the comic strip was discussed with her separately. Eventually I may replicate the comics and post them online and put up a link, but we'll see how it goes! In short, it wasn't my idea, but please enjoy the story!
The TARDIS whizzed through the time vortex, its usual swishing sound emanating through the space, though with an unusual amount of turbulence. After all, the Doctor, who would usually be manning the controls, was busy saying his goodbyes to the TARDIS while his hands began glowing the way they did sometimes.
"I guess it's time for me to go," the Doctor sighed, straightening his bowtie one last time. "See you in a moment, sexy. I've got some regenerating to do. Goodbye!"
With an epic explosion of yellow light, a fair amount of sparkles, and some dramatic music playing in the background courtesy of the TARDIS, the Doctor's transformation began in full. A few minutes later, the glow faded somewhat, and the Doctor fell to his hands and knees.
"Woah," he said, his voice completely different than it had been only moments before. "I'll never get used to that." He noticed the long hair draped down around his face. Standing up, he fingered it.
"More long hair? Well, at least I'm finally ginger. Something new!" Looking down at himself to survey the other changes, he made a startling discovery. There were a couple of things blocking his view that hadn't been there a moment before.
"What the?" he said, confused. Suddenly, the realization of what he was seeing hit him full-force, and his blood ran cold, both of his hearts skipping beats.
"NOOOOOOOOOO!" he screamed in horror. "I'm a GIRL!?"
After several minutes of frantic protests to the undeniable truth, the Doctor pieced himself- well, herself, back together and decided to follow through with a customary wardrobe change.
"Bye-bye, bow tie," the Doctor said sadly, taking off the tie around her neck. Taking a long look at it, she had an idea. "Hello bow!" She wrapped the tie around her head and re-tied the tie around her hair so it looked like a hair bow. That done, the Doctor frowned.
"I guess I should probably tell River..." she thought out loud. "This seems like the sort of thing she ought to know, doesn't it?" The TARDIS thrummed at him. "Alright, I'll go see River. But first..."
The Doctor left the console in autopilot and walked off down a side hall to the enormous closet. She threw the doors to it open dramatically.
"A dress!" she exclaimed importantly, and began rifling through clothes. As all of her previous incarnations had been male, none of those outfits would do, so she headed straight to the rack that was usually reserved for assistants. After tossing aside several choices, she went with a loose t-shirt dress and leggings, then put on some knee-high boots.
"Alright, now that that's done..." the Doctor said, skipping back over to the console. "Time to go!" She fired up the engines and the sound of the brakes screeching suddenly bothered her. Maybe that's why it bothers River. It's a girl thing!
The TARDIS reappeared in the hall across from River's cell. The Doctor opened the door to the TARDIS.
"Sweetie?" River questioned. The Doctor hopped out of the TARDIS with a grimace on her face.
"Hello, River. It's me, the Doctor," she replied.
"Why are you in a dress, and what's with the bow?" River asked.
"Bows are cool," the Doctor said defensively. "Also, I'm a girl."
"Girl!?" River exclaimed. The Doctor pulled out the sonic screwdriver and unlocked the cage, stifling a burp that was the result of the not-quite-completed transformation process.
"Sorry. My new body's a bit strange," the Doctor sighed.
"Mm-hm," River agreed. The Doctor led her back over to the TARDIS. "But... there must be something we can do!" Entering the TARDIS, the Doctor made a bold declaration.
"I have a plan!" she said confidently.
"You do?" River asked skeptically. The Doctor whispered her brilliant plan in River's ear.
"Are you sure that will work?" River asked, raising an eyebrow.
"Yep!" the Doctor replied with a grin, then skipped over to the console and started it up.
"This is not going to end well," River muttered to herself as she found something to hang on to. The TARDIS plunged into the time vortex, as usual, but this time it went into the time vortex at the same place that a past TARDIS- the one that held the recently transformed tenth Doctor- was currently traveling through. The Doctor pulled her TARDIS up alongside the older one and had River keep it there, then went over to the door.
She leapt across the vortex between the two TARDISes, then clung haphazardly to the front of the other. Using her key, she opened the door and let herself in.
"Hello, Doctor!" she said cheerily, walking right up to her old self, who spun around, alarmed and confused. Before he could ask who she was or why she was there, she walked right up to him and kissed him.
With another explosion and flash of light, the transformation, which hadn't been finalized, turned him back into a man. The tenth Doctor was staring at him in shock.
"This is much better," the Doctor said happily. He took the bow out of his hair and fixed it back around his neck. There wasn't much he could do about the dress, so he just went with it.
"Doctor? Are you talking to someone?" a voice asked. Both of the Doctors spun around.
"Oh! Hi, Rose!" the new Doctor said cheerily. "It's nice to see you!"
"Who on Gallifrey are you!?" the old Doctor asked.
"I'm not sure," the Doctor replied. "I'm still cooking, you see. Oh! I have a very important question for you! Am I still ginger?"
"Uh... yes," Rose replied slowly. The Doctor sighed in relief.
"Good. I've never been ginger before, and I didn't want to lose it after such a short amount of time!" the Doctor said. "If you'll excuse me, I must be going." He started walking towards the door.
"Oh!" the old Doctor exclaimed, cluing in to who this stranger was.
"Bye!" the new Doctor waved cheerfully. Rose was still very confused. The Doctor opened the door to the TARDIS and hopped back over to his own. The old Doctor peeked his head out the door, watching his future self go. He continued to watch as the newer Doctor opened the door to his TARDIS and closed it behind him. Then it zoomed out of the vortex again.
"Wow," he said, stunned.
Meanwhile, in the TARDIS that contained the Doctor and River, the Doctor was celebrating his newly-reinstated status as a member of the male gender with River.
"Oh yeah! I'm back, baby!" he exclaimed happily.
"That's definitely better," River agreed. "Now for some pants!"
"Oh... yes..." the Doctor said, suddenly aware of his rather transvestite-looking clothes. He dashed back into the closet until he found some suitable attire, then dashed back out of the closet in a trench-coat and bowler hat.
"What's with the hat?" River asked.
"Bowlers are cool," the Doctor defended. "Now to take you home!"
"Alright," River agreed. With a swish, the TARDIS reappeared in the prison. The Doctor escorted River back to her cell and used the sonic screwdriver to lock her in.
"Bye, sweetie," she said.
"Bye, River," the Doctor replied, and zoomed back into the TARDIS to go off on more misadventures.
I'm posting this as 'complete', but she's made several other unrelated comic strips, and if I ever get around to writing them up, I'll post them here. Some of them are crossovers with Monk or Merlin, but I'll warn you in the author's notes if/when that happens! Let me know if you liked it!
Gandalf- Thanks for pointing out the reincarnation thing! I've fixed it! I must've been thinking of something else while I was writing... Anyway, about the other point, the Doctor isn't regenerating by choice. At the beginning, he is doing it because he has to, it's just not of any importance to the plotline how it happened, so I didn't go into it. When he goes into the vortex to find his old self, his old self is in the process of changing from the ninth Doctor to the Tenth. He himself hasn't stopped the regeneration process. It takes awhile, even after he looks and acts like his new self. So that's why the previous Doctor's regeneration changes his current one. I'm not sure if that makes sense after I've spelled it out, but if it doesn't, sorry! It made sense in my head, and I didn't want it to be as unclear as it was... I apologize for the confusion!