While sleeping, Lt. Col. Hughes recalls meeting Col. Mustang, who was bitter and willing to go as far as human transmutation for what he had done during the Ishval Civil War. Hughes is then awakened by Sheska to inform him that Führer King Bradley has arrived due to an incident at Lab 5. Hughes reveals that the conspiracy is larger than expected due to the disappearance of Lab 5 staff and the recent mercenary attack on Ishvalan refugees, and retrieves Bradley permission to continue the investigation. Hughes also requests that Dr. Marcoh brought to Central for further interrogation, which the Führer has Juliet Douglas do, as only she knows his whereabouts. While explaining the current findings to the Elrics at the hospital, Ed reveals that he has given up the Philosopher’s Stone. Ed decides to look for an alternative method by asking their teacher who lives south of Central in Dublith. Winry wishes to travel because the town of automail mechanics Rush Valley is on the way. After Major Armstrong agrees with Hughes that the Elrics are doing this to protect them as well, the Elrics and Winry wave goodbye to their friends on their train.
Winry soon discovers that the Elrics are not heading to Dublith, knowing what their teacher would do to them if he found out that Ed had become the state alchemist and that he had performed human transmutation. Instead, Ed decides to head south through Rush Valley to the Ishvalan camp where Scar’s group is headed, believing that Scar is hiding something from them and yet he wishes to capture Scar for his killing spree. Scar remembers his meeting with the state alchemist when Rick reveals that he has a visitor who is his master, a survivor of the war, despite Scar’s earlier belief. When the camp is attacked by a biker gang, Scar’s Master reveals that he heard what happened to him and warns him of revenge. Scar leaves his tent and kills several bikers before the others retreat and his master recognizes that the tattooed arm once belonged to Scar’s brother. Back at Eastern HQ, Mustang is on the phone with Hughes, who wants to know why the Elrics were hospitalized, but Hughes avoids the question by stating that Mustang’s transfer to Central HQ will go ahead. After hanging up, Mustang orders Lt. Hawkeye to book them a train to Central so he can find out what’s going on there.
After talking it over with Gracia, Maes returns to the office and has Sheska help him analyze the Ishval War along with the Reole, Xenotime, and Lab 5 incidents. While Hughes messed with what he learned from Ed about what told him by the Homunculi, Hughes remembers something important about the Ishval War after Douglas called to tell him that Marcoh had arrived in Central. Realizing what’s important, Hughes sets out to meet her, but not before shooting Sheska as she leaves. Hughes reveals to Douglas the mystery of how despite her name being the same as the soldier who killed Ishvalan’s child that started the war, although the real Douglas had died two years earlier, the same name was never removed from military personnel records. Knowing that Marcoh is not in the hotel room, Hughes is attacked by Lust from behind. Despite sustaining an arm injury, he uses a thrust knife thrown into her face just as 2nd Lt. Ross—Envy in disguise—arrives to save Hughes.
As Hughes runs, realizing that this corruption goes all the way up to the Führer, he becomes suspicious of Ross when he tries to contact Mustang on the phone. Learning from Warrant Officer Falman that Mustang left for Central with Hawkey, Hughes angrily hangs up the phone and laments that this information could have put the Colonel over the top. Hughes then secretly pulls out another hidden knife and puts it to the side of Ross’s neck, revealing that the real Ross has a mole under her left eye. He stabs the con artist through the throat with a knife. Envy then takes Gracia’s form, distracting Hughes long enough for the changeling to fatally shoot him before leaving. As he falls and dies, Hughes remembers the day Mustang told him he would become the Führer to change the country he would willingly support. The next day, a military funeral is held for Hughes, Elicia is too young to understand its importance. As Mustang recalls his previous attempt at human transmutation and Hughes keeping the Elrics’ recent activities a secret from him, Hawkeye reminds him that it is because of Hughes’ dream of helping him reach the top, prompting Mustang to shed tears for his late friend. . On the train, unaware of what happened shortly after they left Central, the Elrics and Winry talk about Hughes and his family. However, Ed complains about how much Hughes has interfered in their lives, including his boastful personality and obsession with his wife and daughter. Al and Winry talk some sense into Ed, saying that Hughes has always helped and taken care of them and that they should thank him when they get back to the capital. Ed then looks out the window to see the ghostly apparition of Hughes in a regular suit waving gently. Ed continues to stare, though when he sees the platform where Hughes appeared to be, it’s empty on second glance. Ed actually leans out the window, causing both Al and Winry to question if everything is okay. Without mentioning what he saw, Ed dismisses their concerns and eats the last apple pie Gracia made.