I've changed quite a bit, because I wasn't satisfied with it, so here it is, in it's new, hopefully better form.
Enjoy, and please review if you want me to continue.

~K

That's it then. My companion betrayed me, stabbed me and left me for dead in the Tardis. Good thing I didn't tell them abut the regeneration.

Later:

I wake up splayed out on the floor of the Tardis. It appears the regeneration has finished and the first thing I notice is a pressure on my chest. I hope I'm not asthmatic. That would be problematic. My clothes feel heavy and large, splayed all over the ground below me. I must be very slender. I sit up, eyes closed and walk to the mirror. I want to see it all at the same time. I feel the mirror in front of me, and I open my eyes.

"Oh my god." I cry my voice high and feminine. "GIRL BITS!"

This just got way worse.

"I can make something out of this, right?" I ask looking at myself in my too big man clothes. I need to put some new clothes on.

I walk down to the former companion closet, and throw the doors open. The first thing is it's a mess. I can't deal with this. I have to clean it first.

2 hours later.
It's clean, everything's arranged by color.

Now, women usually wear bras, right? How do I know what size I am?

This is going to be way harder than I thought.

Found stuff that fit, now, what to wear?
Pants.

Needs to hold my sonic screwdriver.

Okay, found nice jeans. Nice top, comfy shoes.

Skinny black jeans, purple satin button down, ready.

I dig through the pockets of my old clothes and find my sonic screwdriver.
I put it my pocket and it sticks out. I just can't win today, can I?

Now, I think I'm gonna head to a bar, I need a drink.

I land on the former satellite five, or gaming channel, which has now turned into a space station. I walk toward the flashing neon sign, which is usually where the drinks are. I sit at a stool and order the strongest drink on their menu,

"One pan-galactic-gargle-blaster please." I say, not waiting for the response. The bartender raises his thick eyebrow,

"That's quite a strong drink for such a small woman." He says, as if I would listen. I roll my eyes.

"I didn't come for advice." I reply shortly. He nods, and mumbles,

"Okay, someone might get lucky later." Being a woman sucks.

I get handed the drink and take a deep sip. Someone sits on my left.

"Hello, gorgeous." I turn to look at the man, "You come here often?" I recognize this man from somewhere, but I can't put my finger on it.

"Nope. Not at all." I take another drink from the glowing blue glass.

"A beautiful woman like yourself shouldn't be here alone." I glower at him,

"I can handle it, thanks." he brushes a piece of my curly hair out of my eyes.

"If you don't mind, I'll stay with you." I spit out some of my drink.

"Are you serious?" He smiles, clearly thinking I was being funny,

"Alright, fine, I really just want to keep looking at you, you're captivating." Are men always like this and I just never noticed?

"Suit yourself." He stays and keeps trying to engage me in conversation. I am incredibly terse with him, but he doesn't seem discouraged. Once I finish my drink I face him,

"I have to go." I stand and start to leave.

"Let me walk you at least." There's no shaking him, so I let him come, but if he does anything I'm not comfortable with, I am going to take my sonic screwdriver to his face.

Once we are a few hundred yards out of the bar, he grabs my wrist and pulls me to him and plants a hard kiss on my lips, his hands running up and down my small female body. I push him off.

"I don't even know your name!" He smiles,

"Jack Harkness." My veins go cold. Now I know where he came from.

"I'm The Doctor." He drops my hands and his eyes grow to the size of saucers.
"No!" he stutters, "There's no way." I roll my eyes and start walking away. "WAIT!"

He smiles, "I want proof." I can't believe what I'm hearing.

"Come on, but cut out the flirting." He smiles,
"I was flirting when you were a guy, don't think that's going to change." I look at him and sigh. We walk in near silence to the Tardis.

"Believe me now?" I ask, pushing the door open. He nods, smiling.

"Can I come with you?" I turn, feigning surprise.

"Sure I guess. I could use a companion." I reply dryly.

"Don't act like you don't want me." He taunts. I hit him on thee shoulder,

"Ditto." I point, "The extra bedroom is this way." He looks disappointed.

"No adventure?" I can't believe him.

"I need a rest. Tomorrow." He grabs my hand and kisses it, and I can't believe it.

"Good night." I call, walking down the hallway.

The Next Day

"Morning!" Jack calls waking me from my sleep, and the first thing I smell is breakfast. He made me breakfast. I smile. Then I remember: I'm still a girl. And I promised him an adventure. Where to go… I get up and dress myself in a pair of jeans and a vintage tee shirt from sometime in the early seventies. I don't know where it came from, but I really like it. I walk out to the kitchen and am instantly given a plate of pancakes.

"You didn't have to make me pancakes." I say, almost blushing. He shakes his head,

"We need to eat." I grab a fork and start shoveling pancakes into my mouth. "Gosh Doctor, you're certainly not very ladylike." I stick out my tongue at him.

"So, where do you want to go?" He shrugs,

"Anyone need saving right now?" I listen for just a moment waiting to see if anything calls out to me.

"No. Where do you want to go?" I ask him quickly. He grins.

"Can I go home?" he inquires, thoughtfully.

"Like the fifty-first century?" I counter, thinking, I'm worried about this because of Rose, I know what happens when you mess with personal timelines.

"Yes, I want to see Gray." This stops me. I didn't think he had a boyfriend, or whatever.

"Who's Gray?" I ask as casually as I can,

"Oh, Gray's my brother." He replies, smiling, "Jealous, are we, Doctor?" I blush. I guess girls do that a lot.

"No, just curious, okay, but going into your personal past, there are some rules. Don't talk to anyone I know that's hard for you, but just do it." He nods,

"Also, don't interfere with anything, ever. I don't know exactly when you're sending me, but I don't want this to end with another paradox. I had enough trouble with Rose's."

I crack a little at the end of that, and Jack squeezes my hand reassuringly.

"Let's go." I say, as I pull the lever.