City of Heresy is the third Brotherhood episode, in which Ed and Al reach Reole and dismantle the fraudulent prophet Cornello, whose Philosopher's Stone proves to be a fake handed to him by the homunculi Lust and Gluttony to stir up trouble.
Arriving in Reole, the brothers ask locals about the radio sermons of the prophet Cornello, who preaches the god Leto and claims to grant immortality and raise the dead, a boast that immediately troubles Ed. Watching a public miracle, they conclude his feats are ordinary transmutations and puzzle over how he sidesteps alchemy's basic laws, suspecting they have found their goal. In the church they meet Rose, a devout young Letoist who scorns Ed's faith in science over religion, then agrees to arrange an audience through Cornello's aide Cray.
Hearing that the Fullmetal Alchemist wants to speak with him, Cornello fears the military has come to shut him down and orders Cray to kill the boys, but Ed and Al easily overpower the guards. Confronted, Cornello relies on the red stone in his ring, the Philosopher's Stone, and commands Rose to shoot Ed by dangling the promise of reviving her dead lover. Her shot knocks off Alphonse's helmet and exposes his hollow armor, stunning both Rose and the priest, who then unleashes a chimera. Ed handles the beast, and once Cornello grasps that Ed's limbs are automail and Al is a bound soul, he recognizes a failed human transmutation.
Outside, Al tells Rose that he and Ed only produced a monster and crippled themselves trying to revive their mother, proof that the dead cannot return, yet she clings to hope in Cornello's power. Ed lures the priest to the broadcast room and reveals his own plan: the microphone has been live the whole time, airing Cornello's scheme to seize the country with fearless, faith-blinded followers. Enraged, Cornello attacks with the Stone and suffers a rebound that warps his body; Ed subdues him, and the Stone crumbles to dust, marking it as counterfeit.
Rose confronts Ed at gunpoint, sure he lied about the Stone's destruction, but he insists again that resurrection is impossible, and she collapses in despair until he tells her she must find her own way forward on her own two legs. As Reole's furious citizens storm the church, Cornello retreats and meets Lust and Gluttony, who reveal they only used him, handing him a Stone to stir unrest. When he lunges at Lust, her extended nails pierce his skull, and Gluttony devours the body while Lust frets that Father will be displeased.
The episode adapts the chapters The Two Alchemists and The Price of Life. The title card arrays are the Elrics' human transmutation circle and a simple circle Al uses to fix a radio early on. Unlike the manga, where Cornello already knows Ed's youthful appearance, here he is startled that the Fullmetal Alchemist is not the towering armored one.
The manga reveals Al's hollow state earlier, when Cray shoots off his helmet and Ed hurls it at a guard, whereas the episode has Ed use a guard's staff instead and delays the shot. The mutated Cornello scenes are original to the anime. Ed also references Icarus, the boy whose wax wings melted near the sun, drawing a parallel to his own story.

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In City of Heresy, Cornello is a prophet in Reole who preaches the god Leto and claims he can grant immortality and raise the dead, using ordinary transmutations disguised as miracles.
Edward exposes Cornello in City of Heresy by luring him to a live radio broadcast room, airing his scheme to seize the country and revealing that his Philosopher's Stone crumbles to dust because it is counterfeit.
In City of Heresy, Rose fires at Edward but hits Alphonse's helmet instead, knocking it loose and exposing his hollow suit of armor to both Rose and Cornello.
Cornello's fake Philosopher's Stone was handed to him by the homunculi Lust and Gluttony, who used him only to stir up unrest in Reole before killing him once he was no longer useful.
City of Heresy adapts two manga chapters: The Two Alchemists and The Price of Life.
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