Suspecting General Raven’s disappearance despite a lack of evidence, Olivier Armstrong arrives in Central City to meet with Führer King Bradley. They run into Colonel Mustang and exchange pleasantries as Armstrong suggests that he won’t be able to return to Fort Briggs anytime soon. Roy says goodbye to her and casually jokes that he will send her flowers in the near future. Upon entering Bradley’s office, Armstrong immediately deduces that the Führer will not be fooled by a simple denial of her actions and instead shifts gears to imply that she killed Raven because she thought he was unfit to participate in the Führer’s plan. She claims that Raven too willingly rambled on about “immortal soldiers”, the origins of Amestris as well as Bradley’s own true nature without coercion and remarks that she volunteered to come to Central to take Raven’s place in the plan. Bradley, amused by her response, grants her a position in Central Command in exchange for full control of Fort Briggs, and Olivier states that her troops are strong and will be a valuable asset. In the north at Briggs, however, 2nd Lt. Henschel and Captain Buccaneer remark to each other that their Ice Queen is valiantly infiltrating the enemy and that Central’s cronies underestimated Briggs’ monolithic strength even in the absence of their true commander.
Back in the capitol, Roy meets up with Lt. Hawkeye in the cafeteria and the two take time to catch up and casually shoot the breeze. However, as soon as Riza taps her cup meaningfully, the colonel notices and responds in kind with a pen, as the tone – but not the content – of their conversation shifts to a more serious one. As Hawkeye casually gossips with the Colonel about the past antics of some of their buddies, Roy secretly jots down notes of their exchange and later heads to the bathroom to crack her code in private, only to receive a shocking message from his loyal aide: SELIM BRADLEY IS A HOMUNCULUS.
Beneath Central City, the father sleeps and his thoughts travel back four centuries – to the last years of Xerxes. In a cellar filled with books and bottles, a young man who resembles Edward Elric is awakened from his sleep by a nearby voice, but when he looks around, he sees no one else. But it soon becomes clear that the voice speaking to him is coming from a nearby glass flask in which a shadow ball is floating. Surprised that the young man is not bothered by his appearance, the shadowy being asks him his name, but the boy replies that he is only called Twenty-Three because he is a slave. The creature expresses its encyclopedic understanding of the term “slave”, but when Twenty-Three reveals that it lacks the intelligence to speak on the same level, the creature wonders how it could have been born of such a stupid human, explaining that born of a boy’s blood that it had been taken a few days before for one of his master’s alchemical experiments. In gratitude for being given life, the creature gives its idiotic “parent” a more appropriate name: Van Hohenheim. The creature tries to teach Van how to spell it, but the slave replies that he doesn’t need to learn to read or write in his current position. The Vana creature rebukes this folly, noting that such a mindset will keep him bound in slavery, unable to achieve freedom or rights as a person. The creature offers to give Van the knowledge to rise above his current place, to which the wary slave retorts that he wishes to know what to call his new benefactor. The creature replies that it can simply be called “Homunculus”.
As the years pass, Van learns to read, write, and even perform alchemy, becoming his master’s alchemical apprentice. Van grows to manhood and thanks the Homunculus for his gift of knowledge, noting that now that he has left slavery, marriage and starting a proper family is within reach. The Homunculus mocks the human need to mate and reproduce, but Van explains that it is the pinnacle of human happiness. With the Homunculus still disdainful, Van asks the creature what would make him happy, to which the shadow replies that simply escaping his bottle without dying would be enough.
Soon after, the Homunculus is summoned before the aging King Xerxes, who asks the alchemical anomaly if immortality is possible. Smiling and opening his eyes from the darkness, the Homunculus explains how to create the Philosopher’s Stone, and the king immediately intervenes with it, having a moat dug around the entire nation and secretly ordering the slaughter of entire cities at strategic points in the circle. As time passes and the circle is assembled, the king eagerly awaits his immortality in front of a large, bejeweled mural depicting the five-pointed circle in his throne room. After several years, the circle is completed and the ritual of immortalizing the dying monarch is set in motion. Hohenheim and the Homunculus watch, but Van’s amazement turns to horror as the king and his royal alchemists begin to die one by one. Seeing that the diminutive in the flask is highly amused by this result, Van furiously demands to know what the Homunculus has done, to which the creature gleefully replies that it distorted the circle so that Van and he are standing in the true center. The gate opens and engulfs the entire capital as every citizen of Xerxes has their soul ripped out and condensed in the center. Van and the Homunculus are destroyed at the gate while silence reigns throughout the ancient kingdom. Hohenheim wakes up in the morning to find the capital a ghost town, with soulless bodies lining the streets as he wanders around desperately calling out for his friends. Hearing a voice behind him, Van turns to see his own body staring back at him, dressed in royal robes, and the Homunculus explains that he has created a new vessel for himself using Hohenheim’s blood. In exchange for the blood that gave him life, he declares that he has repaid his “father” with three gifts: a name, a wealth of knowledge, and now a body that will live forever. As Van listens carefully, he is able to hear the souls of countless Xerxesians screaming within his body, which the Homunculus comments that he has divided the population between them.
In the present day, 1914, Hohenheim wakes up from his nightmare on a train to be greeted by his old acquaintances Izumi and Sig Curtis. They talk about Ed and Al as they disembark, but when Izumi starts one of her coughing fits, Hohenheim becomes concerned and waves Izumi’s claim that she’s fine and insists that Sig bring the car. But once her husband leaves, Van comments that Izumi saw the Gate and asks her what the Truth took from her. As she explains the situation of her child’s failed resurrection, Hohenheim quickly plunges his hand into her abdomen and blood flows out. Sig returns and furiously blasts Hohenheim away, but Izumi assures him that not only does she feel much better than before, but she doesn’t even have a wound from just being stabbed. Van notes that he was unable to bring back the organs that were taken as tribute, but he used his skills to reroute Izumi’s remaining internal systems to improve her blood flow, further saying that it is not yet time for Izumi to die. Shaken by his incredible powers, Izumi demands Hohenheim’s true identity, to which he replies that he is the Philosopher’s Stone in the form of a human being.
Up in the northern region, Edward explains the properties of the Philosopher’s Stone to Miles and his men, noting that Kimblee possesses one. Miles notes that he would have expected the legendary catalyst to be larger than a pebble, but when Edward realizes how many people would have to be sacrificed, he expresses his hope that he will never see a larger one.