A filly is picked on due to her heritage but finds counsel in one of her classmates.

Equestria has merged with the Earth and the Conversion movement is still in its infancy. But when a tainted batch of ponification serum is caught in the New York City Bureau, ancient powers begin to stir and awaken. A war that has been waged for untold ages is reignited and threatens to consume the whole world.

Like most convicted felons from London, Daniel Wickerham is sent of to a convict colony in Australia to mine for gold and coal. But he drew the shortest stick and wound up helping at the local Conversion Bureau for the rest of his four year sentence. So how will he fend for himself in this ever changing world? Only time will tell, for he is in for a wild ride.

Humanity is rapidly declining. Ponies came to Earth twenty years ago and now there are plans set in motion that requires the last of the humans to make up their minds about ponification. John Eriksson big businessman and entrepreneur is one of them. After a visit by none other than the element of magic herself he offers to help her spread the message, but this takes a different turn than what he expected and soon he is reunited with old friends, old memories and a 'crazy' coffee addict.

A Conversion Bureau story.

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Discord is defeated and petrified in his stone prision, When Celestia remembers how he used to be, she unintentally wishes upon the stars themselves that he could have had a chance to show his true self.

In Equestria, wishes have a tendency to come true.

Now in an altered form, Discord must discover what role he is to play if he is to remain free and spread the joyous chaos he loves so...

This collection of stories is set in an alternative Conversion Bureau timeline where Mankind reigns triumphant, having destroyed Equestria and sent it back into the sea. The only remnants are Celestia's severed head and the now-docile earth ponies that are made from her blood.

As mankind claws itself back from the brink of extinction, it must build a new society and move forwards into the future, with a changed destiny shared now by two sentient life-forms. In this collection, stories will be spun about sacrifice, loss, and nobility of spirit, of two hands and four hooves.

new title card from http://mi9.com/shattered-horizon-intro_77122.html

Robert Parker is a 24 year old ex-web developer living in New York city. In the wake of the conversion movement, he has seemingly lost everything. Haunted by the same nightmare every night, he soon realizes that he must make a choice.

To those unfamiliar with the Conversion Bureau: it is a scenario created by an author named blaze in which Ponies either appear in the human world or have lived beside humans without incident for millennia. One day, in the face of all the damage humanity has done to its world, the ponies offer a solution: undergo conversion to become a pony and allow the world to be inundated with Equestria's influence: thus healing it and bring forth a golden age.

Many different authors have taken many different approaches to this idea, all of them are worth checking out.

http://www.ponychan.net/chan/fic/res/53616.html (The current thread)
http://www.equestriadaily.com/2011/04/conversion-bureau-compilation.html (The compilation post on EQDaily. *NOT UPDATED*)

One day the Ice King decides to leave the land of Ooo so he can steal princesses without Finn and Jake interrupting. He ends up in Equestria. Finn and Jake pursue the Ice King so they can bring him to justice.

Stephen has a nice chat with the Princess

When Fluttershy finds a human in her backyard trying to eat one of her chickens, she and a majority of the residents of Ponyville only want this dangerous creature as far away from their town as possible.

After a less than stellar first impression, Derpy Hooves and the human struggle to quell the rumors surrounding his diet, and convince the townsfolk that he's harmless.

Will the human be able to make himself meek enough to coexist? Or will he be driven out of town with torches and pitchforks?

Each chapter is told from the perspective of a different pony.