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.

The brothers pursue fugitive May Chang to solve the mystery of why their alchemical powers were rendered inert while she and Scar continued to be able to wield them. Meanwhile, Scar enlists some unlikely help to delve into the secrets of his brother's alchemical knowledge. And the newest, most horrifying homunculus makes an appearance...!