In quite a few of my favorite stories on this site, I've seen that the 'plot/conspiracy to overthrow Celestia' pltline utilized, either as the primary threat or just something in the background. I decided to do my own take on it, taking a page out of "Winning, and the pitfalls therein" by RandomPC, found here

If all you've ever seen of me is what I was, then you don't know me. The mare I've become isn't the filly I was born as, and for all of it, I regret nothing of my new life. This is my story.

Twilight Sparkle has been stuck on Earth, as a human, for a while now. It wasn’t planned, but the human girl that she stays with is at least very helpful. When the stress of finding a way home gets too much for a stranded Twilight Sparkle, her friends look for a way to keep her from going crazy. A few video games won't hurt, will they?

A side story of Merlos the Mad's A Twilight Landing. It takes place just after chapter twenty-four. If you read this story by itself, most of the jokes will still make sense. This may also be considered canon.

I have been informed, that the cover Merlos found for this, is art by MegaSweet!

This story is a sequel to What Have You Done?

Chrysalis, the Changeling Queen, has taken her prize, unhindered by Equestria's precious heroes. Celestia is little more than another prisoner of war now. The Bearers of the Elements of Harmony are lost, and the Elements themselves have turned away from Equestria's plight. As the world they once knew begins to crumble, a single question is asked among the people as they look up at their fallen heroes.

There is no such thing as "miserably ever after," for someone will always be fighting for things to change. Hope doesn't die just because someone's turned off the lights. Truth doesn't vanish when deceit begins its reign, and Harmony can only shine brighter among chaos.
Even as this world falls, we'll work to build it up again.
Even as you lose yourself, you can find greater things within you.
Even as fear rises up like a tidal wave, we'll forge a sanctuary to stand against it.
Even as you break, someone will always be standing there next to you to carry you through it.

Cover art is by Odin-odin.
Story theme (Equestria in Grey) is by Omnipony.
Main Characters are Twilight, Velvet, Discord, Nightlight, Luna, and Chrysalis, in that order.
See you in the comments, my dear readers.

A dud prophecy turns the townsfolk wary of the Elements of Harmony. The only solution to restore friendship: make the prophecy come true and temporarily take the reins as Ponyville's new masters! The Mane Six are going to learn just how hard it can be to be the bad guys...

The plan, he thought, was perfect. Instead of returning to the mortal world as a shade of his former self, King Sombra would transmute his soul into the body of his greatest foe, using her influence and power to destroy Equestria from the inside and take vengeance on the Princesses that stole his beloved empire.

There's just one problem: after her fight with Tirek, Twilight Sparkle changed her address. This turns out to be a much bigger problem than Sombra thought. A Dinky-Doo-sized problem, to be precise.

5th-place finalist in the More Most Dangerous Game contest.

Cover art crudely Photoshopped by me from this and this. I am art and so can you.

Reading by Neighrator Pony

Shortly after the Changeling Invasion, a human wakes up in Chrysalis' body in the middle of the Badlands. Alone, hurt, and starving, she tries to make sense of where she is and what happened. Unable to remember even her own name, she struggles with her identity as she faces the trials of being public enemy to a whole species.

Or, you know, she doesn't. Identity crises are overrated anyways.

While on a trip to Canterlot to do some research, Twilight happens upon a dust-covered book titled Insane Edicts: A Legal History of Equestria. Sure, the book seem innocuous enough, but when she opens it up she discovers that Celestia is far more eccentric than she'd like to believe.

Letters. Everyone writes them, and they're not just for ponies. Be they carriers of serious news, friendly correspondence between pen pals, or declarations of heart and heartbreak, each one is written with a clear purpose or goal in mind.

Celestia uses them to try and keep her faithful student and friends in line, and try to keep an unbalanced world on the straight and narrow.

This is much harder than it sounds.

Now with an audio reading by Lady Tenkage!

Side Stories:

Old-Fashioned Bar Hoppers, featuring Celestia, Mayor Mare, and Granny Smith shenanigans.
Journal of an Adolescent Clone, featuring Sunny and Moony shenanigans since Season 5.

Twilight Sparkle is tired of this nonsense.

Every day, a slew of articles all focused on the minute details of her life invade her beloved newspapers. "Twilight Sparkle Eats Peaches." "Twilight Sparkle Hates Tea." "Twilight Sparkle Uses a Microwave." "Twilight Sparkle Makes Toast." All of it clogging up her precious sources of information from cities across Equestria.

But no more. The time has come to put an end to it, once and for all.

Written with thanks to Marceline from the #FimFiction IRC and for no good reason other than it sounded funny in my head.