(Crossover between the Faith and Fire series and First contact universe, written by Terran117. Please spare some time to read his story.)
Equestria has been under the upstart and idealistic heel of the alien republic known as the UTF for over two years, the once peaceful and blissful country beginning to twist and strain as new ideas and opinions begin to surface among its population. The aliens have begun to bring power to the working class, glorifying the common worker in place of the pampered celebrity. Magic has been given mathematics, and mystery has been given reason.

To many this would bring a better and brighter world, but Equestria was never made to be as other worlds are, and such alien influence has swept over the lands in a violent way, turning neighbor against neighbor in a division of the classes.
The UTF are unstoppable, the princesses are beginning to feel their security begin to thin and Equestria is beginning to yield to their alien masters.

Or so they would be lead to believe.

(Set after season 3, but before season 4. Canon items, characters and locations given detail in season 4 will be paid their respects and noted as still a part of the universe this story takes place in. Imperial forces not of same background as Warhammer 40,000, if confused, please feel free to ask in the comments for clarification)