A take on Humans Acting Villainously: Celestia has won, the barrier and conversion bureaus have wiped away everything humanity had and was.
But uneasy rests the tyrant's crown.
The Newfoals remember legends of things that go bump in the night, and they have decided that now even Celestia must know and fear them too. That there are beings to give even Luna nightmares.
Celestia is merely a Princess, and he is the King.

Yeah! Featured 8/7/14, 8/11/14, 8/12/14, 8/14/14 and 8/21/16. Thank you all.

 Would Canon Celestia and the Mane 6 countenance the Conversion Bureaus and Ponification? In the face of a megadisaster that would sweep humanity from the face of the Earth, I think they would. If only as the lesser of two enormous evils. Our world is out to get us, and only Celestia and the Mane 6 can save Humanity.
A meeting of the group as they put the plan together, and as their worst fears come to fruition.
Author's Note: I don't know if I will continue this. But I encourage others to examine the ideas and play in the sandbox.

A good story should provoke discussion, debate, argument...and the occasional bar fight.
J. Michael Straczynski

Chpt 1) Pinkie and her friends celebrate a new holiday along with the citizens of Ponyville.
Chpt 2) A dark day for Equestria. Who is the new enemy and what do they want?
Chpt 3) Celestia deals with an Arrogant Worm of a pirate
Chpt 4) Applejack, linguist extraordinaire
Chpt 5) Twilight deals with a rumor in a very Twilight way (no, not with sparkly vampires)

Kenny has escorted many of his coworkers to the Conversion Bureau, but he seems strangely reticent. Recognizing someone who has seem too much and gone too far, Twilight Sparkle wants to offer him a happier life. But he has a secret, one that most Equestrians haven't considered.

Another Mystery Crossover: The Conversion Bureau has all but won, and the barrier is closing in. Soon Humanity will be a fading memory. A few last souls are preparing to hand over Earth to its new masters. At the proper place and at the proper time. Celestia is delighted, but should she be?

TVTropes page yay!A human arrives with a house in Ponyville. The Mane Six, and Princess Luna must deal with this new arrival. But not everyone agrees how it should be handled, not everyone agrees on what danger it represents, or the benefit it can be to Equestria.

The inhabitant must also deal with the new rules and conventions of this new world it knows nothing about, as well as the mystery of its appearance, and the incongruities of its arrival.
TVTropes page yay!

An engineer loses his family, and finds himself as a colt in Canterlot, beside Discord's statue. When he realizes he knows the means to defeat Discord, he must do little to disrupt those events. But the rise of the New Lunar Republic demands his action. And the knowledge he can share to help everypony, demands he do something to help. He must do what he can to help his new friends, yet must carefully avoid changing things too much to let the actions to defeat Discord still work.
The Princesses and the buearcracy also realize his usefulness in forwarding their own schemes.

A look into the politics and psychology of the capital, and its people. And theory on the rise of the New Lunar Republic. Celestia faces Luna, and the NLR leadership , alone.

Equestria is an alien world. What if you aren't used to it, or they aren't used to you?
Even when both sides have the best intentions, there are problems. Little problems that aren't so little, ask the Martians in War of the Worlds.

A human arrives in Equestria, and brings death the ponies aren't ready for. Will they have time enough to deal with it?

An ancient, storied evil arrives in Equestria, and joins Fluttershy's menagerie, as a baby dragon.
Will the Mane 6 Discover it in time?
Will they recognize the evil when they see it? Or can it avoid the temptation to succumb to his previous nature?
Will a brave knight challenge this evil with courage and the power of friendship? Helping him face the terror of the memories of his death?

Crossover, but that would give it away.
One Chapter one-shot.
Edit: Fixed several typos, added Alternate Universe tag, and changed the terrible description (to something less terrible, I hope).

Rated Teen for some rather uncomfortable implications.

Definitely a crossover, but spelling it out would be a spoiler. Disclaimer at the end.