Two young boys are working very seriously, drawing on the floor. The older asks the younger, Al, if he's ready and tells him not to be scared. Outside, it begins raining, and the boys place their hands on the intricate circle they've drawn. A gold light emits from it, and we hear narration from the older boy explaining what the basics of alchemy are as the room fills with light. Suddenly, the gold light turns an ominous color, and the boys seem worried. Lightning streaks across the fields as they begin screaming.

A young girl named Winry rushes outside, having recognized Edward's voice, but a small woman stops her when they notice the boys house is glowing. Edward's narration explains further the principle of equivalent exchange, that nothing can be gained without sacrificing something. A man in uniform also watches the boys house, getting soaked in the rain.

Back inside, as the smoke clears, Edward calls out for Alphonse, who seems nowhere to be found. He's in obvious pain as his leg is now missing, and curses that this isn't what was supposed to happen. He hears a choking sound and looks up, into the center of the circle, and is horrified to see a hideous creature, the thing which they have summoned.

Four years later, an older Edward is trekking through the desert, complaining about the sand, with his younger brother Al, who is now a walking, talking suit of armor. The boys have traveled to the town of Liore, in search of something very important to them. The locals tell Ed that the great prophet Father Cornello can perform miracles, among other things, and that he saved their town. Al stands up, accidentally knocking a merchant's radio to the ground, shattering it. Apologetic, Al draws a transmutation circle around the pieces of radio, and placing his hands on it, fixes it instantly. The locals are amazed that they can perform miracles like Cornello. They explain that they're alchemists, not miracle workers, and a mysterious woman recognizes them as the Elric brothers, referring to Edward as the Fullmetal Alchemist. The locals get the brothers confused and think Al is Fullmetal because of his armor, they are shocked to learn the shorter boy is the older brother. Edward violently overreacts to being called short for what won't be the first time.

A local girl named Rose comes by and the boys introduce themselves to her. She takes the Elrics along with her to the temple, and has them wait while she speaks to Cornello alone. Cornello praises her faith, but explains that it will take time to grant her miracle. As she prays before a grave, Al tells Ed that it belongs to her boyfriend, who was all the family she had because her parents died when she was little, and that Cornello has promised her he will bring him back to life for her. Edward is angry that Cornello is leading her on with a lie like that, but Al is hopeful that maybe there is a way.

The boys witness Cornello's 'miracles' first hand, reconizing them as alchemy immediately, but are suspicious of how he can ignore the laws. They explain to Rose about the laws of alchemy; how something can only be created from something equal to itself, and only composed of the same substance, and that Cornello's 'miracles' seem to disregard this. As Cornello brings a dead bird back to life, Rose insists that alchemy can't do something like that, and that it is a true miracle.

In his study, Cornello tells Cray about Edward, that he's the youngest person to ever receive a State Alchemist certification. Cornello explains that they must do something about the fact that the military wants to intervene in their town's prosperity. After Cray leaves to fullfill 'the will of God,' Cornello is seen having a private meeting with the strange woman who knew so much about Edward earlier. She doesn't appreciate the boy being in town and Cornello reassures her he'll get rid of them.

In the chapel, Edward does his best to try to help Rose understand that it's impossible for something as intangible as prayer and faith to bring back the dead, when even science, which has identified every 'ingredient' in the human body, can't even accomplish the task. He continues to denounce Cornello's miracles, stating that scientists are the closest things to God on Earth, so a hack-job like Cornello doesn't have a sliver of credibility. Al eavesdrops from the shadows, annoyed with Ed's constant cynicism, and is surprised from behind by Cray, who shoots off his head and bursts in on Ed and Rose. Cray tells Rose that the Elrics are enemies of their faith and he's only carrying out the will of God, and is surprised himself when Al's empty body speaks to him from behind. Rose is horrified and confused that Al is an empty suit of armor. He explains it's their punishment for trespassing on God's territory and that she shouldn't be afraid, but she runs from them, angry with herself for doubting her faith and believes that the Elrics really are evil.

The boys follow her down a long, dark flight of stairs which lead to a large empty room. Cornello is waiting for them there, and Ed wastes no time in mentioning 'the stone' which Cornello understands to be the red ring on his hand. Edward's suspicions about The Philosopher's Stone had been correct, which explains how Cornello was able to perform his miracles. Edward demands he hand it over and instead Cornello tells him about how he restored the town when they thought God had forsaken him and wants to know why the military would want to destroy all that. He is surprised to discover that Ed has pursued the Stone of his own accord, and Rose is outraged that Ed would ruin the faith of the entire town for his own personal gain.

Cornello tells the boys if they want the Stone, they'll have to take it from him, and turns the floor into sand so that they won't be able to draw the transmutation circles they need to perform alchemy. He introduces them to a chimera he made, and as it charges Edward, the boy transmutes a lance out of thin air without a transmutation circle, shocking Cornello, who then uses his ring to enlarge and distort the small bird on his shoulder into a monster that flies straight at Edward. He makes it a point to narrate his kick to the bird with his left leg, and the punch he lands in the birds face with his right arm, which sends the bird backward across the length of the room, knocking it out. Cornello is visibly shaken at Edward's strength, but moments later seems pleased when Ed can't escape the first chimera's attack. Rose looks on in horror as the monster chomps down on Ed's right arm. The chimera seems to be having trouble though, and Ed flings it off him, and kicks it across the room as well.

The mysterious woman has apparently been watching from the shadows with a rotund companion she calls Gluttony. Cornello is aghast that Ed survived his chimera attacks and realizes that his limbs must be fake. Edward rips away his coat, revealing his right arm and left leg are indeed prosthetics, and tells Rose to look at him, explaining that it's what happens to people who attempt to bring someone back from the dead. Cornello scoffs at them for being crazy enough to attempt something forbidden like that and understands why Edward's State Alchemist title is "The Fullmetal Alchemist."

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