The hobbled Elrics return to their childhood village for the first time in four years. As the Rockbells construct Ed's new limbs, the boys sift through the ashes they left behind. While Al comes to the fearful realization that his memories are fading, Ed visits his mother's grave, and both must redefine their view of family and home.
After the explosive finale to Lab Five, Ed and Al wake up in the hospital, once again in pieces. Winry travels to Central to make repairs, and is enraged by the brothers' refusal to tell her the truth about their lives. Meanwhile, Al's recurring questions about his existence come to a boil. Was there ever an Alphonse Elric? Or are his memories and soul alchemically created lies?
As Al runs from Ed and Winry, desperate to know the truth about what he is, mercenaries swoop into the Ishbalan encampment where Scar is recovering and massacre helpless refugees-an attack the military may have condoned. In a chain of events, Al finds himself side by side with Scar, on a renegade mission against the state that Ed represents.
Ed and Al claim they've quit their search for the Philosopher's Stone and board a train heading south. Meanwhile, Lieutenant Colonel Hughes' investigation of Lab Five leads him to a startling discovery of military corruption and conspiracy that could topple the entire national government-- and put Hughes in considerable danger.
Winry drags Ed and Al to the famous Rush Valley, the auto-mail capital of the world, where mechanical limbs are a shockingly common sight. Amidst workshops and street-smart swindlers, they encounter a tough girl named Paninya, who confronts Winry with an important question: Why is she helping Ed, if he doesn't even care?
Ever since Ed and Al attempted human transmutation, they have desperately avoided one person: their childhood teacher, Izumi. Bearing dreadlocks, an iron will, and incredible alchemic skills, she is horrified that Ed and Al used her teachings to violate nature. Now she has caught them, and is shipping them back to her hometown for a frightening interrogation.
It was the only clue Izumi offered, as she dumped young Ed and Al on the island of Yock: "One is All, All is One." It was perhaps the most ancient tenant of alchemy, but what did it mean? And how would it help these children survive in this savage place-with no food, no shelter, and a beast lurking in the woods? Years later, the lesson must be relearned.
As the Elric brothers are leaving Yock Island, a strange boy emerges from the foliage, with no memory of how he arrived. Inexplicably, he can perform alchemy without a transmutation circle. Even stranger, he can transmute his own body, merging with his surroundings! Izumi is compelled to take care of the child, but Ed has other plans.
The search for Scar gets a forward leap as a former military officer spots him in the southern slums. Elsewhere, the amoral Lt. Colonel Archer makes his move for the mysterious wild boy, who he believes is a homunculus conspirator. Infuriated by the arrest, Izumi leaps into action, single-handedly attacking the military with her staggering alchemic power.
In the chaos of the crumbling headquarters, Izumi successfully escapes with the boy. But it's too late-Envy has revealed the truth to the homunculus child, and his personality is quickly changing. With Izumi's secrets exposed as well, the Elric Brothers try to stop her heartbroken plan of atonement, converging on a cold stone altar on a lonely island.
After a dangerous battle with Wrath, Izumi has all she can take of Ed and Al's reckless pursuit of their goal. She sends them to meet Dante, the alchemist who taught Izumi decades ago, and also knew their father. But there is little time for idle chat, as Envy, Sloth and Greed have all entered the vicinity.
The boys are separated when kidnappers take Al to their hideout, leaving Ed frantic to find his brother. Izumi steps in to help her protégés as always, and finds they've learned something from life she could never have taught them alone...responsibility.
Major Armstrong battles Greed's men in the sewers in an attempt to save Al, while up above, Ed escapes the military's clutches for a showdown with Greed. As Lust suggests the battle is part of some larger plan, Greed morphs his body into an impervious shield, and swears Ed must kill him if he wants to see Al again. But is there another way?
Ed, Al, and Winry continue on their journey to Ishbal, uncovering more of the mystery as they travel along. But how much do Ed and Al really want to know? Are they ready to hear the truth? Lust and Gluttony meet Wrath for the first time and quickly set out on the Elric Brother's trail. Will Ed and Al reach their destination before they're overtaken? And if they do, are they ready for what they'll find?
Someone high up the military ladder has ordered an investigation on Colonel Mustang. What follows is a one-of-a-kind look into the daily affairs of the Flame Alchemist and his loyal (and often ridiculous) staff. Is there a haunted warehouse in Central full of soldier-killing zombies? Is Havoc lonely? Does Major Armstrong have a sister?
Forced to go on foot after their vehicle explodes, Al questions Ed for the first time about the direction of their mission, prompting a heated brawl that sends the brothers stomping off in opposite directions. Back in Central, Sciezka and Winry follow the clues that Hughes left behind, and come face to face with the deadly, shape-shifting Sloth.
With the half-snake, half-woman Marta as their guide, Ed and Al arrive at the ruins of Ishbal. Their shock at the devastation is magnified as Marta divulges the real cause of the Ishbalan war, and the dark series of events that led to her transformation into a chimera. Once again, Ed and Al must question everything they believed.
Marta has found Kimbley, whose betrayal led to the death of her friends. Realizing revenge is pointless, Al tries to stop Marta, and jumps into the fight. In Liore, Ed goes head to head with Scar, and uncovers the full truth behind his past. Finally, in a heart-wrenching exchange, the identity of the Seventh Sin will be revealed, and a friend of the Elrics will die.