There exist those with special abilities to manipulate objects and transform them into other objects called the Alchemists. However, this manipulation process comes at a price, since the basic alchemy rules state that something with equivalent value is needed to perform the manipulation.
The renowned alchemist Edward Elric loses his little brother Alphonse in an accident. Edward manages to contain his brother's soul in a large piece of armour suit, but by doing so Edward loses his arm and leg. And so the brothers set out on a perilous journey to regain their original bodies.