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.

In the midst of heated battle, Ed, Envy and Prince Lin of Xing are swallowed whole by the homunculus Gluttony. When they finally escape, they find themselves face-to-face with the "father" of the homunculi, who offers Lin immortality as the new Greed. Meanwhile, Colonel Mustang learns the military's corruption goes all the way to the top, and the truth of what really happened in the Ishbalan War is revealed.