Welcome to Equestria!

Ponyville. It used to be beautiful, and some ponies will tell you that it still is, but...it isn't. Ever since the breakout of the Coltsavar Mutation, it was now quite hideous. Black, pulsing growths were everywhere on any patch or organic material, like grass or trees. Said organic material was replaced by erratic black growths pulsing and leaking, with long free strands hanging from the structures, sometimes touching the ground to create a look of torn skin, hanging on be mere threads. Everything was dark, and any colour that dared exist in the poisoned town was overshadowed, poisoned, and dulled by the spore-ridden fog that covered the town, and all of Equestria, quite thickly.

You might be thinking, 'Well, that's fucking cliche, and edgy as shit!' And you'd be quite right. However, the problem with the Coltsavar is that it doesn't modify thought. It modifies the body by mutating it sometimes uncontrollably and horribly. At first, the infected were burned as horrifying creatures, but it became apparent that they were still ponies, at least in mind, when the mysterious infection swept the nation. Soon, everybody was infected and mutated within a year. All except Twilight Sparkle, who quarantined herself and dressed herself to leave nothing showing. Single-respirator gas mask, long coat, underclothes, waxed clothes, an undersuit, cut tail and mane, everything to keep herself safe....and it worked. For 5 years, she hasn't been infected by the horrible disease. During this, the Equestrian Crusader Advisers were created. They are to eliminate any massive growths present across Equus.

Now that we're done with this shitxposition, we can get to some actual plot.