Although Colonel Roy Mustang is furious at Ed and Al for running away without telling first, but thanks to Major Armstrong's gentler approach, they explain to him that they ran because Führer King Bradley is a Homunculus (Pride) and therefore part of the conspiracy over the Philosopher's Stone. They also reveal that Juliet Douglas is a Homunculus as well, much to Sheska's relief as she thought that she was an alien. They still keep Al's new status as the stone a secret, however. Mustang has Armstrong work on sending the rest of his search party back to Reole while he heads to Resembool. Along the way, Ed and Al learn that Jean Havoc and Kain Fuery have already been sent back, with Ed apologizing for what he did. The subject changes to his pocketwatch, to which Al admits that he lost it after Solf J. Kimblee threw it at Scar and some Red Stone fragments came flying out, which Mustang realizes that Frank Archer was responsible. He admits that they used the Red Stones before during the Ishval Civil War under Basque Grand's authority as transmutation amplifiers. During their argument, Al accidentally causes another transmutation, knocking him into a river, although the Elrics quickly cover up the truth to avoid revealing the stone.

After learning of the reappearance of their father from Denny Brosh upon their return to the Rockbell Automail house. Al is excited to see him, but Ed is angry enough to deck Hohenheim with one punch for flirting with Maria Ross (and later kicks him in the stomach after misinterpreting his question of whether he still hates milk as a statement that he hadn't matured enough). That night, Hohenheim reacts when he overhears Ed describe Lyra as wearing the same obnoxious perfume he has smelled on his father, and Al's relief that she had safely escaped Dante's house (after her apparent murder by Greed). Later, he has a private conversation with Mustang. Mustang mentions that the Führer is married and has a son in addition to having seen pictures of him when he was younger. Hohenheim reveals that Homunculi originally do not possess their human shape when they are born, and must be fed human lives through Red Stones to gain it, and that the Führer can likely alter his appearance to make it look that like he ages like a human. He reveals that Selim is likely adopted since a Homunculus cannot reproduce. He also mentions that due to Laboratory 5 having produced Red Stones, it is likely that someone is raising 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, in which Hohenheim reveals because the Homunculi come from the other side of The Gate. Against Ed's wishes, he decides to spend the night with his father.

Hohenheim reveals that Al's body was lost and it's possible to transfer his soul to another's body which he cannot do. He learns that reversing Equivalent Exchange can bring his body back, although he does not mention Sloth. The next day, Hohenheim disappears, and Mustang, as he leaves with Riza Hawkeye, wants them to stay in hiding while he deals with the search party that has just arrived in Resembool. He also promises to look into the claim of the Führer being a Homunculus. Pinako then sends the boys 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 a special Black Ops group had actually started the war. He then realizes that the Homunculi were the real instigators of the war so someone could create the Philosopher's Stone. Once Sheska mentions that Maes Hughes was likely killed for learning too much, Ed and Al are surprised that Hughes is dead and Ed prepares to chase after Mustang, but has to be restrained. Pinako talks some sense into him that Mustang didn't tell him so he wouldn't try to seek revenge. Even though Sheska admits how wrong she was for not trusting him, Ed still hates him.

Hohenheim arrives at the same church where the Homunculi are. He recognizes Lyra immediately as Dante, her soul now residing in Lyra's body, and that she had been controlling the Homunculi all along. Hohenheim, knowing his body is near its limit, offers to tell her why her new body is already decaying rapidly in exchange for a promise to leave his sons alone, and proves his point by exposing a part of Lyra's skin that has already rotted, much to Lust's surprise. While Alphonse mentions to Winry that the search party is gone, Edward assigns himself a grisly task--desecrating his mother's grave to obtain a piece of her corpse to use as a weapon against Sloth.