The story focuses around two brothers, Ed and Al. They lose their mother to an unknown illness, and try to re-animate her using alchemy. The story states a principle of "Equivilent Trade" within the practice of alchemy. It states "You can not gain something without sacrificing something else of the equal value", more or less the Law Of Conservation. Another rule of alchemy is that human restoration is a taboo. In the attempt to revive their mother, they gather all the chemicals that a human body is comprised of, except the soul. The transmutation fails, Al loses his body, Ed loses a leg, and consequently an arm while binding Al's body to a suit of armor.
The two set out to obtain the Philosopher's Stone, which will supposedly allow them to perform human transmutaion. In hopes that they can get Al's body back, restore Ed's limbs, and bring back their mother.