Hearts of stone

After Twilight Sparkle and her friends "mysteriously" disappear, Equestria is taken over by Stonegaze- a magic-hating earth pony dictator.

After the order is given to wipe out all unicorns, Equestria's magic, desperate to return, takes the form of a gene, affecting several creatures, giving them some sort of enhanced ability. Stonegaze won't make the same mistake twice. Defects are being captured left right and centre, but it's up to Polybius Shard, her brother, and the rest of the outcasts to fight for their freedom...

Otherwise they might find themselves as test subjects for their rest of their lives.