Truth is the first casualty of war.

The world is in flux; new ideals, groups and technologies permeate every level of society in this age of discovery. The field of augmentation has allowed ponies to improve themselves in ways that were unthinkable a generation ago. Yet, for every benefit, there is an inverse. A griffon civil war rages on the borders, feeding the profits of mercenary companies. Rising populations have forced the rich and poor ever further apart. Harmony is dying.

Mortally wounded after a fatal attack on her laboratory, an earth pony researcher is augmented against her will and sent out into a chaotic world in search of answers. But as her quest unravels this chain of events, she discovers an ancient conspiracy that will shake Equestria to its very core.

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TVTropes Page

My Little Pony crossed with Breaking Bad:

Several years in the future, a middle-aged Twilight Sparkle is diagnosed with a terminal disease. Facing hospital bills and having severed all ties with Princess Celestia several years ago, and making a meager living as a magic kindergarten teacher, she realizes that she needs to make more money to be able to support Spike.

She sees her opportunity and teams up with Pinkie Pie to produce and sell the popular new illicit drug "Crystal Spark", but runs into difficulties keeping her activities secret, especially since Applejack and Rainbow Dash are leading the Ponyville unit of Princess Celestia's elite anti-drug task force.