Rainbow awoke bright and early the next day, which means she just managed to wake up before the afternoon. Such was this a rare occurrence that she actually managed to get her weather management done for the day, before her boss had to wake her up, surprising both the stallion and her colleagues.
All in all, this started out as a pretty good day for Rainbow. She managed to get her work done, so the sky was nice and clear with a smattering of clouds scattered about in preparation of the storm scheduled in a few days. Rainbow decided that the rest of the morning could be spent relaxing as opposed to being reckless like she usually is.

...but then she remembered that the morning was already over, so....

"Rainbow Dash!" Twilight's voice called from behind her, she overshot where she was supposed to go, Twilight was looking at her in wonder, "I wasn't expecting you so early."
Rainbow shrugged, "Eh, you know me, excited for science and stuff."
Twilight looked her up and down, before simply stating, "You fell off something you were napping on didn't you?"
Rainbow raised her eyebrow inquisitively, "Yeah, how did you know?"
"You're not as animated as you are usually, and you just said you were interested in science," Twilight shook her head and smiled, "which means you're tired and delusional, that and you just told me."
Rainbow pursed her lips, "You got me there."

suptg.thisisnotatrueending.com/archive/24642609/images/1367797028600.jpg

"You're not as animated as you are usually, and you just said you were interested in science," Twilight shook her head and smiled, "which means you're tired and delusional, that and you just told me."

Twilight anyone who agree to do science with you usually is.
That's true...
Ya think Twi?

The tattoo just bounced off the walls and danced with the newer sounds, all this just added to the stark emptiness of Twilight's castle.

The tattoo?
Oh my gosh!!! A fake cutie mark!!!Get an exorcist!!!

Rainbow nodded her head, letting the overwhelming feeling of all these machines pass her by. As they traversed through the metallic forest of machines Rainbow briefly remarked on the different kinds of machines there were. There was one that looked like a microscope, except on steroids, another that looked like one of those super cool plasma ball things, and one that just looked like a refrigerator.

The sight of the refrigerator looking contraption confused her, "Hey, Twilight," she said to her friend, stopping their motion briefly, "what's that machine there?"

Twilight looked at Rainbow incredulously, then she smirked. She cleared her throat and explained exactly what that machine was, "It's a sealed container that uses a multi-cooling infused sapphire array to condense and evaporate the liquids inside, providing the items within a longer life before nutritional decay." Twilight then walked up to it, she put her hoof on the handle and pulled it back to open it.

A tiny delicate wave of coolness touched at Rainbow's hooves. She frowned once she realised what it was.

"It keeps my food cold."

"I know what a fridge is, gees, I was just... never mind."

Twilight aren't we supposed to keep food outside of the lab?
Oh right...

Twilight smiled at Rainbow's question, "It's a gender swapping potion."

You do realize that you'd get more test subjects if you just said that in your flyer right?
What could you possibly mean...
You mean you didn't know?
Know what?
Equestria has the highest amount of cases of Gender Disassociation Disorder in all of Eden.
The more you know.

I enjoy the deleted scene.

Rainbow's wails of agony quickly shifted to groans of pleasure mixed with pain.

So close to being a perfect transformation. I don't understand why she would have pleasurable feelings here when a cock forcibly growing sounds painful. I imagine it would be very sore, at the least.

Bonus points for the use of the word 'tattoo' in a non-body-art context.

"I would really have to assume the opposite judging by the way you were hurtling towards the castle," she shook her head as she placed her friend on the ground, "if it wasn't for my passive acceleration dampening array I placed around the castle, you'd be a Rainbow pancake."

Yeah, because god knows how many times Rainbow Dash has tried to suicide-crash straight into Twilight's home. If I had a penny for every time Rainbow Dash has done that I'd be...well, I don't know really because I lost track of all the times RD has done that so...yeah.

Also, convenient magic thingie is convenient. One sin, as the Sin channels would say.

Well thi-

intense pain,

Maybe I'll just skip this chapter.

Normally, I would give more detail, but I am rather tired, and I have work tomorrow. Please ask me about anything, I will usually answer the same day.

Chapter 1:

It ensured that she was woken up complete, if the fall didn't do that already.

Probably meant "completely."

shook her head to try and rid her mind of the pre-nap fog that was about to conquer her mind.

in front of the two guards posted to guard the door.

Duplication feels weird. There are more of these throughout the story. I think it's important that you recognize the pattern, rather than fix every individual mistake.

as she reached up so feel where the pain came from.

causing the pleasure to increase passed the threshold of pain

"past"

Chapter 2:

but now he's mind was definitely certain

her warm breath ticking his ears

"Tickling," I bet.

Before long, she once more slamming down onto him.

Bad tense, or missing word.

Her nethers clenched at Rainbow's penis, trying to milk it for his glorious substance, but it was for naught, he was yet to climax.

Great place for a semicolon.

yet her hind quarters was oh so ready

He sped up quicker, he began letting out short breaths of air though his nose as he pumped in and out of Twilight with feverish pace.

"Through," and it should be two sentences.

she could feel the pleasure amounting again

an action the expended more energy that he believed he had