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.

Ed, Alphonse and their mechanic Winry go south in search of Izumi Curtis, the master alchemist who taught the brothers how to use alchemy. But in the boomtown of Rush Valley, an encounter with a pickpocket turns them down a different path in search of an auto-mail blacksmith whose handiwork is the best that Winry has ever seen. Then the action flashes back to the past to show how Ed and Alphonse first learned alchemy...