Scar is recovering from an injury he sustained in Lab 5 at Camp Ishvalan, cared for by Rick and his older brother Rio, though he focuses on his experiences instead of taking medication. However, a group of mercenaries, including former Lab 5 guard Barry, attack the camp with the intention of genocide against the Ishvalans, with their leader using a specialized backpack that can use alchemy to massacre the area. While the boys’ grandfather believes this destruction to be Ishval’s doing, Scar knows it is the work of evil men. Al walks through the rain in Central, reminiscing about his argument with Ed, wondering why he didn’t answer and also if his mother’s memories are also false. Meanwhile, Rio and Rick are on the run for stealing food, and during their escape from the store owner, Rick trips and loses his necklace. Coincidentally, they hide in the same place Al is and he recognizes them as Ishbalans. While Winry and Ed work to find Al, Ed still upset about what he wanted to tell Al, Al is taken by the boy to the sewers where the Ishbalan camp has moved. While there, Al and Scar meet, which Scar explains to the boy’s grandfather that he is not with the army and they both keep the details of how they know each other’s secret. Once Al agrees to his grandfather’s wish to keep their location a secret, Al learns that the reason for their hiding is the State Army’s genocidal intentions against them.
However, when Rick realizes he dropped his mother’s locket during his earlier escape, against Rio’s advice, Rick goes to retrieve it with Rio, Scar, and Al right behind him. While chasing the boy, Scar comments to Al that it’s easier for him now that Al broke up with Ed. Rick finds the locket, unaware that mercenaries are following him and Rio, who get permission over the phone from Juliet Douglas to find their hideout. On the way back, Al learns that the memento from their mother is sealed so it cannot be opened, and that Rio is very bitter towards his mother. Returning to the sewer entrance, Rick is captured while checking to make sure no one is around. Scar and Al fight to get rid of the mercenaries, but escape with Rick. Al contacts Second Lieutenant Ross, who learns about the mercenaries and where their hideout is. As they drive there with Scar, along with Rio and his grandfather because of their loyalty to Rick, Al overhears Rio mention that their mother left them. When Ross informs Ed of what’s going on, Rio reveals that during the Ishval Civil War, he and Rick went undercover while their mother prayed to the Ishval and witnessed the military break down their front door. Rick saw their mother run into the room in fear seconds before it exploded, killing her. Rio reveals that despite the locket being nearby, he swore to protect Rick and never mention what happened that day.
Despite the mercenaries expecting them, Al and Scar use their alchemical powers to launch a surprise attack to quickly rescue Rick, and while Scar faces their leader, Al confronts Barry again. Barry taunts him, further weakening Al’s resolve, and just as Barry takes advantage of knocking Al down with a bazooka shot, Ed arrives to stop Barry’s attack. Once Winry arrives as well, she reveals that she and Ed were worried about Al, and after creating a wall to protect themselves, Ed reveals to Al the thing he was reluctant to mention, if Al hated him for putting him in the armor . With renewed determination, Al fends off Barry’s next attack and tells Ed he hates him, and Scar uses his tattooed arm to block the mercenary leader’s alchemical attack before defeating him. When Ed identifies himself as the State Alchemist to the shock of the leaders, Barry attempts to attack Ed as revenge for being partially responsible for his soul being put into a new body, but Scar intervenes and blows Barry’s armor in half. A blood rune from the top half of Barry’s armor fuses with the backpack in an unstable alchemical reaction, causing an explosion and taking Barry with it, though the mercenary leader narrowly escapes the explosion.
However, one of the knives from the backpack hits Rick, who survives thanks to the locket that forced him to open it. Their grandfather noticed some pills stored inside and revealed that their mother had an eye disease that affected her eyesight, which explains the boys’ rough upbringing as she tried her best despite her condition. When a tearful Rio realizes that she was looking for them that day, he quietly lets go of his past hatred towards her. The leader of the mercenaries is murdered by Douglas’s mysterious water powers when he questions her about Ed’s involvement in their operation. The Elrics and Winry say goodbye to Scar and the Ishvalans, who are about to travel across the water to join the next group of Ishvalans. Rio thanks Al for his help and they both promise to hold on to their memories, and Scar answers Al’s previous question that he is human. Ed asks about the rumor of a Philosopher’s Stone in Ishbal, to which Scar replies that there has been interest, but refuses to comment that one is being made. Al convinces Ed to let Scar travel with the group as they need him, and after the Elrics watch the Ishvalans leave, they talk about their own memories as they return to the city with Winry.