Winry and Sheska arrive in Resembool and Sheska is surprised at how rural it is. However, a stranger who was on the train with them mistakes Winry for her mother Sara, so the two escape. While at her home, her grandmother Pinako tries to find out what Winry has been up to since she left, when an unknown man appears, both Winry and Sheska go into hiding. The man says he can’t find his house. Noticing Winry’s nervousness, Pinako points out that while Winry was too young to remember, the man is Hohenheim, Ed and Al’s father.
Ed and Al head across the desert as they are now on the run and cannot return to the army, with both the Führer and his secretary being homunculi. This confirms Al’s suspicions about Julie Douglas’ true identity: the result of their failed attempt to transmute their mother. When Ed refuses to talk about it, their argument causes part of the Philosopher’s Stone in Al’s body to create a random transmutation where he sees the gate. Ed realizes that he must avoid touching his brother to prevent further draining of the stone’s power, which would result in Al’s body completely disappearing. He decides they should head to Resembool first, where he needs to get something to help him fight the homunculi, even though it’s the first place the army will look.
Back around the site of the former city of Reole, the injured survivors of Scar’s giant transmutation field are being loaded onto a train bound for Central. Among them is a heavily bandaged Archer, whose body was badly mutilated during the transmutation. Lieutenants Breda and Havoc inform Colonel Mustang and Lieutenant Hawkeye of what their search has revealed. Führer Bradley arrives and pretends to believe that the Elrics were partially responsible for the destruction of the city. He accuses them of secretly working with Scar and causing the deaths of 1,000 soldiers, avoiding the fact that it was Archer’s own ambitious recklessness that contributed to the deaths of the soldiers. Mustang volunteers to arrest the Elrics, a request the Führer grants, albeit with the warning that there will be accountability if he fails. Troop Mustang and Major Armstrong leave with several other soldiers.
On a train bound for Central, Führer (Pride) meets Gluttony and Sloth in a secret compartment and reveals that they restrained Lust for allowing the Elrics to escape.
In Resembool, Winry finds Hohenheim around his wife’s grave. He notices her looking at her mother’s grave and explains what happened to her as Pinako watches them. At Winry’s house, Sheska answers the door and comes face to face with Lt. Ross and Sergeant Brosh. Winry returns home as Sheska argues with Brosh, accusing him and Ross of stalking her and Winry from Central. As they are shown the remains of Elric’s household, the girls learn that Ross’s Communication friend delivered the news that the Elrics have become refugees, which is why she and Brosh are here, though Ross can’t explain it. fully. Once Hohenheim makes a suggestion about a nearby river, Winry realizes that it could be where the Elrics come from. He heads off with Sheska while Ross and Brosh stay behind to hinder the search party as much as they can. As Ed and Al travel downstream, they hide from Falman and Breda. However, Havoc and Fuery spot them and Havoc holds Ed at gunpoint. Ed angrily tells Havoc that he’s done with the military and holds the tip of Havoc’s gun with his automail hand; Havoc and Fuery wince in pain as the weapon explodes and ricochets, injuring them both. The horrified Elrics apologize before attempting to escape, but are cornered by Falman and Breda, whose uniforms are then turned into balloons by Ed while he and Al escape. Mustang and the others arrive after the Elrics get away and meet up with Fuery and Havoc. They speculate on how the Elrics will travel, with Mustang getting some matches from the injured Havoc before they leave. When Winry and Sheska appear on a mechanical bike, Hawkeye quickly knocks it out with a well-aimed shot and takes them into custody (hostage). With the girls as their prisoners/lever, the military group continues their search. Winry and Sheska start sniffing at Mustang, who ignores them. Winry accuses Mustang of betraying Ed after helping him get into the army, and Sheska comments that all he cares about is his rank. When Winry brings up the subject of her parents’ execution at the hands of Mustang, Hawkeye stops her.
The military party catches up with the Elrics. Ed admits again that he is done with the army. Despite Ed using alchemy to create a giant wave of water to render his flame alchemy useless, Mustang uses the matches he took from Havoc to replace his gloves and combines his alchemy with Armstrong’s to prevent the Elrics from escaping. When they are trapped and hear Winry’s screams to stop the fighting, Mustang confesses that he executed her parents on command during the Ishval Civil War when they refused to stop healing the Ishvalan rebels. However, he reveals that after this horrific experience, he vowed never to follow such senseless orders again, and that it was this event that led him to seek the rank of Führer for himself. He also reveals the reason he took this mission to find out why the brothers ran away without coming to him for help first.