Slowly and painfully, Twilight walked in the vast desert. Her hooves are cracked from years of running and sneaking. Patches of fur have fallen from her coat, what remains has been bleached to a pale lavender or charred black. Old scars and new wounds line her body, staining the nearby fur in varying hues of red, ranging from crimson to dark maroon.
Her friends, distant memories. It has been 5 months since she has heard another's voice. She has never felt so lonely, so tired or sad in her life before. The feeling of pain is void. All she wants now is to live and survive, sleep by day and travel by night.
But not even the shade of the black night can hide or protect her from them. It was they who destroyed Equestria. They took away her friends and her happiness. These monsters, once known as Celestia and Luna, ruled over Equestria in complete harmony, until something happened to them. Something changed them...
Ok well I'll be honest and say its good for a first try, however, you could improve it slightly. As this prologue is, it looks like, how most people refer to something like this, a 'wall of text.' Though small, I feel you can separate it out a bit. Kind of like this:
The things I've bolded are some things I think you could improve on. I'll go over them in order so bare with me.
It may read better if you replace that comma with a semicolon because the following sentence doesn't quite flow well on all on its own.
You could just omit 'split' and the sentence would still read fine.
The 'walking, running, sneaking' part sounds a little off and would be better if you just said 'running and sneaking.' I know walking and running are different but by just saying 'running' in place of the two, one can read and figure out that Twilight is constantly on the move which is the point you're trying to get across.
The next bolded one has a problem with receptiveness. "It has been 5 months since she has heard any voice other than her own, and 3 days since she has heard hers." I get what your trying to say, but you already stated how she has gone 5 months without hearing anyone's voice except hers, and after that you state again how long she has gone without hearing her voice specifically. This make the sentence very awkward to read. It can be fixed with a little bit of rewording.
The comma here should be replaced by a semicolon since the following is almost a complete thought.
'They' should be omitted. It reads better without it.
The period should be replaced with a comma since the following sentence can be connected with the conjunction, 'but.'
For the period here, i think an ellipse, -> ... <-, would fit nicely here for a nice pause to add a little bit of a drama to the story so when I read it I'm going, "Wow what happened to them...why are all evil and yadda yadda."
Overall it did catch my interest but only after I 'forced myself' to read this one, giant paragraph. Just fix up the prologue up a bit, space it out, and it should be good.