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.

Barry the Chopper, the psychopathic killer whose soul is encased in a suit of armor, has been captured by Colonel Mustang's troops. Fearing he will reveal the Philosopher's Stone conspiracy, Gluttony and Lust decide to kill him, using Barry's own original soulless body to track him down! Though Colonel Mustang has anticipated their moves and set up an ambush, Gluttony and Lust prove too powerful and easily fight their way through to Barry, who is being protected by Al and Lieutenant Hawkeye. In a terrible battle, a badly injured Colonel Mustang sacrifices all in a last-ditch attempt to stop Lust!