In the southern slums, the Ishbalans were placed on a train bound for military camps. However, the train is delayed due to water supply problems caused by the Elrics. Surprised when Rick and Rio mention what the military did, Ed and Al talk to the Ishbalans about what Scar said about the Philosopher’s Stone being created in Ishbal. While Rio denies it due to his newfound hatred of Scar, Scar’s Master mentions an old man who is an Ishbalan exile in Kishua who should know something about the stone, and requests that Rick and Rio lead the Elrics there. With the hose spinning out of control as the ice is removed, the State Army is able to remove the Ishbalans from the train and the Elrics escape with Rick and Rio in the confusion. However, Sgt. Fuery notices them and forces Ed to knock him out. Winry arrives with a tractor she repaired and they use it as a getaway vehicle when they are spotted by Lt. Havoc.
Later, as they travel by train to the old man’s house, Ed brings up the topic that he no longer wants Winry to accompany him and Al on their adventures and should return home to Resembool. When Winry objects, pointing out that she keeps Ed’s automail, Al agrees with Ed due to his temptation to remove Wrath’s limbs and return them to Ed. He couldn’t try because Winry was present, though it was impossible, though Ed admits he could have done it to help their mission. Ed then points out what Barry Chopper said three years ago about killing someone easily, and then brings up the subject of accidentally killing Majhal, as well as almost killing the Central Prison convicts in Lab 5 to create the stone. Knowing that he will face Scar again, who Rio agrees should die, Ed points out that since he and Al will have to face more dangerous battles, it’s better not to have anyone with them to get in their way.
After narrowly dodging a train, the group arrives in Kishua and upon seeing the remains of the battle that took place, Rick suffers from a flashback until Rio snaps him out. When it becomes clear that Rick and Rio cannot go to the old man’s old man due to their religious upbringing, Ed and Al head alone and can only find a marking that is the same as Scar’s tattoo. Lt. Hawkeye then fires at them from outside, knowing that Ed will dodge it to fix Fuery’s injury. Tracking Lts. Hawkeye and Breda escorting the Elrics to the military tent, Winry admits to the boys that Ed can fix the mess. Inside, Breda reveals that Colonel Mustang and Officer Falman have already returned to Central Command, surprising Ed with how quickly Mustang left. As they debate how the Ishvalans were treated, Hawkeye reveals that no Ishvalans were killed, with the only real casualty being former lieutenant Yoki, whom Ed remembers and is surprised to have died. At that point, Hawkeye admits that Mustang used his flame alchemy to force the extremist Ishvalans to retreat to prevent casualties on both sides.
Hawkeye reveals that while they transport the Ishvalans to the south, they must first find out who killed Yoki and keep several of them locked up. The Elrics realize that the old man is there and learn that he has been placed in protective custody due to his status as an outcast. Winry learns from Rick and Rio that the exile is an Ishvalan kicked out of Ishval for breaking an alchemical taboo and is forbidden to interact with regular Ishvalans and have a mark on his face as proof. The boys also reveal that Scar is now an exile as well. Winry changes the subject and asks about the boys’ mother. Rick mentions that their mother was kind and worked in a hospital during the war.
When the Elrics talk to the old man, he reveals that Scar and his brother asked him about the stone before, and that Scar’s brother didn’t create the stone years ago because he was too kind. The Exile then revealed that alchemy was known as a great art that was once followed in Ishval until it was banned. The old man then reveals that there is no difference in creating the philosopher’s stone between their different styles of alchemy, only the number of human sacrifices is different when a powerful alchemist collects the sacrifices to create the stone, which is the only method. In the desert, Scar begins to carve a symbol with a huge stone that is chained to his body, promising to never sleep again. The old man returns and reveals that when Scar saw the army in the area, he realized that the stone was the only thing strong enough to stand up to the army. When asked if he would become an outcast as well, Scar admitted to the old man that he was, since technically the victims of his people were in his tattooed arm. This knowledge offended Rick and Rio, who were with Scar, and Rio demanded that Scar leave immediately.
Winry learns that Rick and Rio actually knew her parents and dated them, until their mother mentions that Urey and Sara Rockbell were killed by a state alchemist who controlled fire, which Winry realizes was Mustang. Back with Hawkeye and Breda in the tent, Ed and Al look at the photos of the wounds that killed Yoki. The Elrics realize that only Lust’s Ultimate Spear can cause these wounds, and when they realize that she was Yoki’s killer, Ed mentions that Major Armstrong and Colonel Archer can back up their story. The Elrics leave the tent as some soldiers restrain Winry, Rick and Rio. As they talk it out, Ed reveals that the Ishvalans will not be punished for any wrongdoing, even if they are still sent to the camps, and Ed decides that his next goal is to find Scar before he does something terrible. When Ed hesitates to admit that he wishes to kill Scar, Rio accuses Ed of hating the Ishvalans. Seeing if the boys are afraid of his automail, Ed admits how afraid he was of the red eyes of the Ishvalans when he first met Scar in Central three years ago. Ed recognizes that instead of following their emotional responses or what they have been taught to believe, they should find their own answers.
When Ed asks what Winry is going to do, she decides to go to Central to visit the Hughes family and travel with Hawkey. As Ed and Al watched the train leave, they took the tractor and headed to Ishval first. On the train, Winry brings up the subject of her parents, to which Hawkeye replies that soldiers must kill, even if it means following orders that are irrational. Hawkeye also reveals that despite her distaste for soldiers, she chose to stay once to protect someone (Mustang) of her own free will, which was her choice. Meanwhile, Sloth introduces Wrath to Lust and Gluttony and orders them to head for the Elrics as they are heading to Ishval. Laziness reveals that if they discover the secrets of the Ishval Civil War, the Elrics will no longer wish to create stone and may need to be killed. At the Hughes house, Winry learns from Gracie about Maes’ death and how he wanted to support Mustang’s dream, even though Winry can only cry.