Infected

It's a story after Twilight Sparkle became princess, you see this story tells the tale of an unknown virus, infecting all that lives and breaths, turning them into robots of pure destruction.

Like the above says, but this will tell ya more. Months had passed after Twilight became princess, but her student Artic Storm had a vision of chaos, saying that a new threat was coming soon. That threat was none other than Red Shadow, a mare who created the virus.