If you have no idea what the Fall of Equestria universe is, I suggest reading Twipet's Fall of Equestria: Sun's Setting
http://www.fimfiction.net/story/211341/fall-of-equestria-suns-setting
To get an idea of how the AU got started.
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Moonshade, daughter of Princess Luna, niece to Princess Celestia and cousin to Princess Cadence has spent two years searching for… something, what it was can only be guessed at. Her travels have taken her beyond the borders of Equestria, into lands barely explored.

Now that she is ready to head home, her first experiences that something is wrong comes when she runs into a camp run by the previously unknown caribou.

The Shadow Princess now has one goal, one that may make the ponies who once feared her reevalutate their thoughts and feelings towards her if she succeeds.
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This story does follow my events of the Chronicles of Moonshade arc, even thoughthat story is set in the actual MLP universe (with some slight AU to it). It includes a background for Moonshade, so while reading it maybe recomended, it isn't necissary. Here is the link for the Chronicles story. http://www.fimfiction.net/story/275690/the-chronicles-of-moonshade