Knowing the truth behind the prophet's power, the Elrics seek to unseat him and reveal the truth to the citizens of that desert city. They also seek to steal the source of the power for themselves, until they discover a secret about it that even the prophet didn't know.
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?
With everyone reeling after the fight between Ed and Greed, Lust can't shake two questions from her mind. Where did she come from? And where will she go when she is dead? As if to answer, she sees a familiar man in a crowd. Years ago, she helped him use alchemy to combat a strange plague that was turning villagers into stone. And his mere presence produces unexplainable memories of a former life.
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.
Massive bloodshed seems inevitable in the mounting stand-off between Scar and the military. As Ed tries to get the Liore people out of the city before the destructive alchemic reaction begins, he is confronted by Wrath and Sloth. And back in the heart of Liore, Scar, Kimbley and Al are enmeshed in a climactic battle that none of them may survive.
Scar emerges from the grisly battle, determined to create the Philosopher's Stone using Archer's soldiers as the final ingredients. Desperate to stop the massacre, Ed continues his underground fight in hopes of reaching the surface in time. And Lust follows Scar through Liore's war-torn streets, seeking the final truths about Scar's origin before he performs his ultimate transmutation.
In the aftermath of the Philosopher's Stone creation, Ed and Al embark on a dangerous journey home. The Fuhrer declares the Elrics to be fugitives of the state, responsible for the deaths of nearly a thousand soldiers, and wants them captured-- dead or alive. Can Mustang's troops intercept the boys before they fall into the wrong hands?
With the mastermind behind the seven sins organizing a plan to capture the boys as well, Ed and Al must convince Mustang's faction that the Fuhrer is not what he seems. The strange reappearance of their father only complicates things further, as we learn he has his own score to settle...one that goes to root of this entire conspiracy.
The confrontation between Hohenheim and the leader of the Homonculi continues, and we finally discover the "truth behind truths." As Al receives a mysterious phone call, Ed proves he will do whatever it takes to stop the Homunculi-even defile his mother's grave. And back in Central, Colonel Mustang decides to challenge the entire military leadership on his own.
The brothers are separated, and both are in peril. Al meets with the increasingly deranged Tucker, while Ed returns to Dante's mansion for any clue that could lead him to the Homunculi's leader. Meanwhile, the Fuhrer sends Mustang and Armstrong to command his northern campaign. Will the boys have to fend for themselves in this increasingly dangerous struggle?
Tucker used Al's power in a new attempt to resurrect his daughter, and the transmutation has disintegrated part of Al's armor. Anxious to stop the Philosopher's Stone from losing more potency, Sloth captures Al. But Ed arrives to stop her. With Sloth, Wrath, and Lust all on the scene-and all with different motives- it's time for a homunculi showdown.
Al is in the hands of the homunculi, and Ed has precious little time to find him. Nearby, Mustang reveals his daring strategy, turning the Fuhrer's attempt to silence him into a push for revolution. After a rapid chain of events, Ed and Mustang find themselves in a car together, giving the two stubborn alchemists a chance to close old wounds.
What is the real secret to alchemy? What fuels transmutations? Is Equivalent Exchange the defining principle of the world, or a fabrication that give false hope to the weak? All answers will be revealed, as the confrontation with the homunculi's leader sends Ed to a place that could shatter his entire understanding of alchemy: the other side of the Gate.
Ed returns from beyond the Gate, leaping into a desperate battle with Envy to stop the mastermind and set Al free. But can Ed deal with Envy's true form? In the Fuhrer's mansion, it's the Ultimate Eye against Flame: Mustang versus Pride. The future of the state is on the line, and an alchemist is going to die.
The Elric brothers have been on a long and difficult journey, seeking to regain what they've lost. Enemies have been toppled, friends have been buried, and the state has been remade. But it's not over yet. In this climactic final chapter, Equivalent Exchange gains new meaning, as Ed and Al demonstrate how much they will sacrifice for each other.