In the church, the boys encounter a young Letoist woman named Rosé, who chastises Edward's agnosticism and balks at his assertions regarding science's superiority over faith. Changing the subject, Edward requests that Rosé secure him an audience with Father Cornello and she gladly obliges, relaying the message through the Father's adjutant Cray. However, upon hearing that the famous Fullmetal Alchemist wishes to speak with him, Cornello becomes anxious and suspects that the State Military has sent an agent to shut down his operation. Under the Father's orders, Cray attempts to kill the boys so as to keep them from taking action, but Ed and Al easily subdue him and his guards, prompting Cornello to appear before them personally. Edward accuses Cornello of using alchemy to fool his followers with the help of the red gemstone on his ring - the Philosopher's Stone. Continuing to deny his deceit, Cornello orders Rosé to shoot Edward, promising to answer her prayers and resurrect her late lover if she continues to act under his command in the name of Leto. Blinded by grief and false hope, Rosé levels Cray's gun at the Elrics and fires, knocking Alphonse's helmet clear off. But when the headless armor boy regains his footing and reveals his empty nature, both Rosé and Cornello are shocked, driving the phony prophet to resort to his trump card - a chimera created with the Stone's power. Edward displays his ability to perform alchemy without a circle and engages the beast, but his transmuted weapon proves both inadequate and unnecessary when the creature is unable to either claw through his left leg or bite through his right arm. Seeing that Ed's limbs are automail and recognizing that Al is a disembodied soul bound to a suit of armor, Cornello immediately understands that the cause was a failed attempt at Human Transmutation - alchemy's greatest taboo. Edward explains to Rosé that his injuries are the result of trying to resurrect the dead and advises that she not pursue such a path. Ed challenges Cornello to face them himself, but when the priest attacks with the power of the Philosopher's Stone, the boys are forced to flee with Rosé, escaping to the church's upper levels.

Outside, Alphonse explains to Rosé that he and Edward had tried to bring their mother back to life, but had only succeeded in creating an inhuman creature and maiming themselves horribly, leading them to understand the truth - that it is impossible to bring someone back from the dead. Even so, Rosé persists in believing that Cornello's power may be enough to perform a successful resurrection. Chasing after the Elrics' trail, Cornello comes across Edward seated casually in the broadcast room. Fullmetal asks why Cornello has built a fake church around himself if he already has the power of the Stone and the priest responds that his true goal is to use religious faith and phony miracles to bring up a flock of devout followers who don't even fear death; with such a powerful force at his disposal, he plans to overthrow the current government and place himself as the head of the country. Unfortunately for him, Edward reveals his own "true plan", letting Cornello know that the broadcast microphone has been on the entire time, airing the priest's whole plan to his no longer hapless flock. Furious, Cornello attempts a fresh attack with the Philosopher's Stone, but it results in a rebound, mutating his arm and then his entire body to a grotesque form. Edward manages to subdue the powered-up Cornello through force, but when he demands that the false priest hand the Stone over, it crumbles to dust, leading Ed to the conclusion that Cornello's stone was a fake as well.

Edward meets Alphonse outside and explains the situation, but Rosé appears and demands the Philosopher's Stone at gunpoint, accusing Edward of lying about its destruction so as to use on his mother. Edward asserts once more that dead people cannot be resurrected and Rosé collapses in despair, wondering how she is supposed to go on now that her last hope has vanished. Edward tells her that she needs to figure that out for herself and that, with the two strong legs she has, she can move forward on her own.

As the furious people of Reole march on the church and demand an explanation from the Father, Cornello sneaks back to his inner sanctum lamenting that the Fullmetal Alchemist has ruined all his plans. He is met by Lust and Gluttony who scold him for letting his elaborate plan fall apart right at the end, but reveal that they were only using him and gave him a Philosopher's Stone so he would stir up trouble in the region. Cornello, furious with the two mocking him, charges Lust, but is killed instantly when her razor-sharp fingernails extend and impale him through his skull. While Gluttony eats Cornello's body, Lust laments that their Father will not be pleased with this outcome.