A crossover in the same vein as The Conversion Bureau: Wrong Universe, set in the universe of Magic: the Gathering.

http://www.fimfiction.net/story/32753/The-Conversion-Bureau%3A-Wrong-universe

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.

A tragic accident robs Jay and many of his friends of their parents. Seeing no alternative aside from a life on the streets and poverty, they enroll in the Conversion Bureau program to emmigrate to Equestria. When Jay finds out that his close childhood friend and crush, Chloe, is going as well, he takes it upon himself to win her affection before the end of their ten day stay.

A trip to the Pine Barrens to research the Jersey Devil takes a turn for the worse.

When a mysterious flower is brought to Ponyville from the Everfree forest, many ponies begin experiencing incredibly realistic dreams. Most residents of the small town choose to lock themselves away, living in the dream rather than reality. When Twilight recruits the only other ponies still awake to help her, they discover the dark truth of what has befallen their kin.

In the many years after the Conversion Bureaus' shutdown, Twilight Sparkle is tasked by the Princesses with finding the last living human on Earth, Isaac Hamilton, and learning the story of his past. What she hears is a tale of loss, tragedy, joy, and the discovery of one's place in the world. But how much longer would that place last with what Twilight has to tell him?