In an alchemical transmutation gone wrong, Edward Elric lost his right arm and his left leg, and his brother Alphonse lost his entire body, ending up as nothing but a soul in an empty suit of armor.

Equipped with mechanical "automail" limbs, Edward becomes a state alchemist of the military and starts a long journey across the nation of Amestris along with his brother, trying to restore their bodies to their original shape by finding the so-called Philosopher's Stone, which is said to give an alchemist the ability to overlook the law of Equivalent Exchange.

At first the Elric brothers have that one goal in mind, however, as their journey continues they find themselves fighting for something that is much, much greater than they could have ever imagined.