Lyra and Rosé descend a secret staircase in an old church where Lyra explains that he used to belong to an older religion that is no longer practiced and once caused the death of many people in a religious conflict. At the bottom, the homunculi Laziness, Anger, Gluttony and Lust await their arrival. Sloth berates Lust, who is still imprisoned, for allowing the Elric brothers to escape, though he reminds her that it is not her mission to take them out when Lyra and Rosé arrive.
While Colonel Mustang is angry with Ed and Al for running away without seeking him out for help first, with Major Armstrong’s gentler approach, the Elric brothers explain that they ran away because Führer Bradley is a homunculus (Pride) and therefore part of the conspiracy . over the Philosopher’s Stone. The Elric brothers add that his secretary Juliet Douglas is also a homunculus, much to Sheska’s relief as she thought he was an alien. However, the Elrics still keep Al’s new stone status a secret. Mustang tasks Armstrong with sending the rest of his search party back to Reole while he heads to Resembool. Along the way, Ed and Al learn that Havoc and Fuery have already been sent back, with Ed apologizing for what he did. The item changes to his pocket watch, which Al admits he lost after Kimblee threw it at Scar and some redstone shards flew out, making Mustang realize Archer was responsible. He admits that they had used the red stones before during the Ishval Civil War under the Basque Grand as transmutation enhancers. During their argument, Al accidentally causes another transmutation and knocks him into the river, though the Elrics quickly cover up the truth so as not to reveal the stone.
After learning from Brosh about their father’s reappearance after returning to the Rockbell Automail house, Al is excited to see him, but Ed is angry enough to punch Hohenheim once for flirting with Ross (and later kicks him in the stomach after misinterpreting his question about whether he still hates milk as a statement that he hasn’t matured enough). That night, Hohenheim reacts when he overhears Ed describe Lyra as wearing the same unpleasant perfume he smelled on his father, and Al’s relief that she escaped Dante’s house safely after her apparent murder by Greed. Later, Hohenheim has a private conversation with Mustang. Mustang mentions that the Führer is married and has a son, in addition to seeing pictures of him when he was younger. Hohenheim reveals that the homunculi do not originally have their human form when they are born, and must be fed human lives with redstones to obtain it, and that the Führer can probably change his appearance to appear to age like a human. He reveals that Selim is probably adopted since the homunculus cannot reproduce. He also mentions that due to Lab 5 producing red stones, it is likely that someone is keeping them and having them teach others how to make them due to their inability to perform alchemy. Al appears and asks why they can’t, which Hohenheim reveals is because the homunculi are coming from the other side of the gate. Against Ed’s wishes, Al decides to spend the night with their father.
Hohenheim reveals that Al’s body has been lost and it is possible to transfer his soul into another’s body, which he cannot do. Al learns that reversing the equivalent exchange can bring his body back, though he doesn’t mention laziness. The next day, Hohenheim disappears and Mustang, as he leaves with Hawkeye, wants the Elrics to stay in hiding while he deals with the search party that has just arrived in Resembool. He also promises to look into claims that the Führer is a Homunculus. Pinako then sends the Elrics and Sheska into the basement to hide. While there, they bring up the subject of Juliet Douglas, and once Sheska mentions that she started the Ishval Civil War, Ed reveals to her that the war was actually started by a special Black Ops group. He then realizes that the real instigators of the war were the Homunculi, so someone could have created the Philosopher’s Stone. Once Sheska mentions that Hughes was probably killed because he learned too much, the Elrics are horrifyingly shocked that Hughes has been dead since they left Central. The Elrics angrily prepare to chase after Mustang because he didn’t tell them, only to be held back by Sheska and Winry. Pinako coaxes Ed that Mustang didn’t tell him not to seek revenge and only hid the fact so the Elrics wouldn’t be blamed for Hughes’ murder, and that seeking revenge wouldn’t be something Hughes would want. they approved. Sheska and Winry regain their respect for Mustang when they finally realize his true determination to be a better man, just as he promised Hughes, and even though Sheska admits how wrong she was to not trust Mustang, Ed still can’t let go. his anger and hatred towards him.
Hohenheim comes to the same church where the homunculi are. She immediately recognizes Lyra as Dante, her soul now residing in Lyra’s body, and that she has been controlling the homunculi all along. Hohenheim, knowing that his body is close to its limit, offers to tell her why her new body is already rapidly decaying in exchange for a promise to leave her sons alone, and proves his point by exposing some of Lyra’s skin , which has already rotted a lot. to Lust’s surprise. While Alphonse mentions to Winry that the search party is gone, Edward sets himself a gruesome task – to desecrate his mother’s grave in order to obtain a piece of her corpse to use as a weapon against the Sloth.