Sentient transmutation, the greatest taboo amoung all alchmeists. Such alchemy could lead to terrible consequences to whoever attempted it, such as the Elric brothers: Edward and Alphonse Elric.

After a failed attempt to resurrect their mother, Edward lost his front right leg and his left hind leg while Alphonse lost his entire body. Realizing their mistake, the brothers set out on a quest to restore their bodies.

After gaining a new lead on the philosopher stone, a powerful stone capable of enhancing alchemy, the brother duo set their sights on equestria, unaware that they'll get more than they bargained for.

This story takes place in a alternate universe where equestria is a neighboring country of amestris (the fake country the series takes place in) and all the humans are replacing with sentient creatures found in equestria (such as ponies, dragons, griffins, etc).

Also, while this might be a poor excuse as to why, all the FA characters have the same names because names work differently in amestris than they do in equestria (such as the name doesn't hit one's talent, and that they have a family name that's passed on).