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.

Automail engineer Winry is captured and held hostage to force Edward to do her captor's bidding. Hawkeye discovers the disturbing truth about President Bradley's son. Our heroes have fortuitous and not-so-fortuitous reunions with old friends and enemies. And multiple intrigues and double-crosses ensue as some plot to save the world while others scheme to destroy it.