In the present, at Central Command, as Colonel Roy Mustang prepares to head back to his jurisdiction in East City, he is met by Lt. Colonel Maes Hughes, who gives him the final report on the Isaac McDougal incident - a report which notes the Freezing Alchemist's abilities as involving Alkahestry, a mysterious art from the eastern nation of Xing. On Mustang's way out, Maes asks Roy why he made Edward a State Alchemist when he knew that a position in the military would inevitably lead him down a dark and hellish road. But as Roy remarks to himself that those boys have already been through hell, he reminisces on the events that led him to the boy who would be known as the "Fullmetal Alchemist".

Four years earlier, Lt. Colonel Mustang had arrived in Resembool with 2nd Lt. Riza Hawkeye to scout out some potential recruits for the State Alchemist program and discovered the horrific, bloodstained remains of what was unmistakably a Human Transmutation Circle in the Elric home. Furious, he had set out to find the culprit and found the young Edward Elric - crippled from the loss of his leg and maimed from the loss of his right arm - in the home of their neighbor. While he had originally come to censure the little alchemist, his discovery that his brother Alphonse had survived the experiment as a soul bound to a suit of steel armor changed his demeanor to one of astonishment. Sitting down with the Elrics and Pinako Rockbell, Mustang explained that Edward's skills would be more than enough to qualify him for the State Alchemist program, where, once enrolled, he would have resources at his disposal capable of leading him to discover a method of restoring his and his brother's bodies to normal. Pinako objected, remarking that she had seen and buried the inhuman monster that the boys had transmuted with alchemy and chastising Mustang for tying to pull them back into such nightmarish affairs. Outside, young Winry Rockbell was speaking with Riza and mentioned that soldiers had taken her parents away from her and now were trying to take Ed and Al away. However, Riza responded that the choice to stay or go remained with the Elric brothers alone and that no one would force them to act. When asked by Riza why she became a soldier, the 2nd Lt. responded that she had done so in order to protect someone. As Mustang and Hawkeye took their leave, Riza remarked that Edward's eyes had looked so full of defeat, but Roy responded that he had seen fire in those eyes.

On the train, in the present, Edward remembers the day he had decided to go through with the operation to install his Automail limbs in order to move forward as Mustang had suggested. When asking how long the rehabilitation process would take, Edward responded to Pinako's answer of "three years" with the proclamation that it would only take him one. A year later, after the process had finished, Edward revealed to Alphonse that he had gained the ability to transmute without a circle, just like their teacher. But when Ed asked Al if he could do the same, due to his own sojourn into the Gate, the younger Elric responded in the negative, appearing not even to know of what "Gate" his brother spoke. Shortly afterward, Edward ventured to Central City to take his certification test, for which the Führer, King Bradley was personally in attendance. After displaying his skill as well as his nerve by staging a mock attack on the Führer, Edward was given his State Alchemist certification and the symbolic sobriquet "Fullmetal Alchemist".

As dawn breaks in the present, the Elrics' train arrives in Reole, where Edward hopes that their journey will come to an end - with the Philosopher's Stone.