Katherine Bosley, who never really cared much of what others thought of her, was having a really, really crappy day. But when she unwittingly gets thrown into Equestria, and finds herself marked as public enemy #1, she's had just about enough of taking the crap the universe throws at her.
Someone is gonna get torn a new one.
And it may or may not be her.
Will she survive? Probably not, but she'll be darned if she doesn't go out with a bang.

Inspired by The Rise of Darth Vulcan and F*** it, I'm having fun.
I realized there were no stories of this newfound genre that have a girl villain. So here you go.
Mild language- I don't like getting in the habit of dropping F-bombs.
Please feel free to point out any grammatical mistakes I make. Now edited by GDQuirm, who puts up with my excessive and exhaustive use of the semicolon.

5/17/14- How the heck did I get in the feature box again?- 30 minutes later, it's over. :/

After a thousand long years, Princess Luna was finally freed from Nightmare Moon and welcomed back to Equestria. But she became Nightmare Moon for a reason, didn't she? What if Luna wanted to take over Equestria even before she succumbed to jealousy?

Having returned from the moon, she secretly writes her efforts to seize the throne and notes the challenges that stand in her way. But if there's one thing that hasn't changed over the last millennium, it's the fact that she can't recognize a losing battle when she sees one.

(Thanks to SpaceCommie for editing!)

A Metroid Crossover

A meteor, resistant to magical manipulation, crashes in Equestria, Planet Equis, and soon spreads an unknown poison throughout the land. Containment is all but failing and the Princesses have little power to stop the spread of the Great Poison. The Elements of Harmony are of little use as no knowledge exists of this threat that consumes all life. Help comes from a certain Hunter, clad in metal.

Samus Aran will not only fight for her life as always, but her own sanity as well as these ponies that she begrudgingly starts seeing as allies. New horrors and abilities await her as a reason to fight slowly festers within her, possibly unlocking something she had been denied for so long: Friendship.

Notes and Resources:

This takes place after Echoes. The events of Corruption will have not happened yet. In terms of MLP, consider everything up to and including the Crystal Empire. Princess Twilight does not exist here, etc. The official Metroid Timeline can be found here.

As well, this story references the manga in many places. Reading of it is not required and I try my best to explain the context, but if you're interested, both volumes can be found here.

EDIT: This story was written over two and a half years, beginning in 2013. You'll probably notice the difference in writing as the chapters progress.

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

Twilight Sparkle, Princess Celestia's most prized and faithful student, is being sent to Ponyville to learn about the magic of friendship.

And she's not happy about it.

Hear what Celestia has to say back! Check out the spinoff:
Responses To A Disgruntled Friendship Student by keaton-furman-prower

Still want more? Have a multiverse spinoff by MixMassBasher, my contributing writer for Seasons 5-9.
Letters From Across the Disgruntled Multiverse

Editing by Neko Majin C.

Disclaimer:
The following is a work of parody, and is protected as Fair Use under section 17 U.S. Code § 107 of US Copyright Law. My Little Pony: Friendship is Magic and all affiliated characters are property of Hasbro Inc.