In an alchemical ritual gone wrong, Edward Elric lost his arm and his leg, and his brother Alphonse became nothing but a soul in a suit of armor. Equipped with mechanical "auto-mail" limbs, Edward becomes a state alchemist, seeking the one thing that can restore his and his brother's bodies...the legendary Philosopher's Stone.

With all the pieces now in his possession, the homunculus father executes his master plan as Edward and the others watch in horror. When the dust settles, the entire world has been reshaped. With the help of Hohenheim, the Elric brothers lauch a desperate final attack, but is it all too late...?