Ed, Greed, and Lan Fan have a difficult time fighting Pride, who gained Gluttony's powers after devouring him. Working with Hohenheim, Al allows himself to be captured by Pride in order to grab him so that Hohenheim can trap Pride in a mountain of soil where there is no light, preventing him from using his shadows. Meanwhile, Kimblee begins to move just as Scar's group is told about the bombing of Bradley's train. As the Promised Day begins, Greed goes to Central on his own while Ed's group and Scar's group meet up again to devise a plan. In Central, Roy and his subordinates begin to attack soldiers while using Bradley's wife as a hostage. However, the military higher-ups give the order to kill everybody in the group except for Roy.

As Team Mustang and Mrs. Bradley gets cornered by Central soldiers, Team Charlie, Mustang's old Ishbal squadron, intervenes and saves them. Team Mustang continues their attack on Central without killing anyone. Meanwhile, the Briggs soldiers lead by Buccaneer join the battle. Soon Team Mustang begins to run low on ammo, and they are saved by an ice cream truck driven by Rebecca and Maria Ross. Mustang calls whoever ordered Ross to return from Xing, and he is surprised to hear Havoc at the other end. During all of the chaos, Ed's group manages to sneak in underground through the Third Lab, where they split up. Ed, Scar, Darius, Zanpano, and Jelso go in one direction while Hohenheim and Lan Fan go in the other direction. However, at that moment, one of the Generals awakens the Army of Immortals.

The Mannequin Soldiers awaken and kill the general. As Ed's group arrive at the door where Al had fought against Lust, the mannequins emerges from the door and they turn out to be immortal indeed. Meanwhile, Olivier is attacked by Sloth, who had been ordered to kill her. Al and Heinkel learn too late that Pride had been sending a secret message from banging on Al's head and are soon attacked by Kimblee, who frees Pride from his imprisonment. In the sewers, May is also being attacked by mannequins and when Envy manages to merge with them, he is able to return to his regular form. As Olivier struggles against Sloth, Alexander rescues her and joins the fight. Al transmutes his legs off in order to help Heinkel, who then gives him the Philosopher's Stone that Kimblee previously discarded. Al uses it to restore his legs and face Pride and Kimblee.

Al begins using the Philosopher's Stone to battle against Kimblee and Pride. He manages to trap Pride once again, but is taken by surprise by Kimblee when he starts using his own stone. Meanwhile, as the Armstrong siblings start to gain the upper hand over Sloth, Sloth begins to use his true strength and reveals himself to be the fastest homunculus. Although Al gets apprehended by Pride again, Heinkel, having been healed by Marcoh, manages to deliver a fatal blow to Kimblee. Yoki arrives to rescue Al and the others and head towards Central, while Pride consumes Kimblee. As Alex manages to temporarily impale Sloth on a spike, both he and Olivier are attacked by Mannequin Soldiers. Meanwhile, May fends off both Envy and the Mannequin Soldiers, and Ed's group, overwhelmed by the soldiers, are joined by Roy and Riza.

Mustang's team has Mrs. Bradley interviewed on live radio. With the power of radio and the help of the Ishbalans, word of a supposed coup d'état spreads, giving the rebels support from the citizens, while Briggs launches an attack on Central HQ. Meanwhile, Roy manages to destroy the Mannequin Soldiers surrounding Ed's party by burning them to ash. May lures Envy into a trap in the upper levels, causing them both to fall below into the chamber with Ed's group. Envy reveals that he was the one who killed Hughes, infuriating Roy who seeks to get revenge. Ed's group moves onward as Roy fights Envy, but Ed gets concerned that Roy may end up being consumed by his own hatred. Envy is no match for Roy and flees for his life. Upon seeing Riza heading towards Roy for backup, Envy gets an idea. Roy later encounters Riza, who aims a gun at his back.

Riza sees through Envy's disguise as Roy and shoots him until the real Roy arrives and mercilessly incinerates the homunculus, reverting him back to his parasitic form. Before Roy can kill Envy, Ed, Riza, and Scar persuade him to let go of his anger and his need for revenge, for Amestris cannot be ruled by someone consumed with hatred. Envy becomes outraged by Roy's change of heart and rants about why everyone does not kill each other, trying to goad them into doing so by pointing out all of the terrible things they have done to each other. Ed determines that the reason Envy hates humans is because he is jealous of their capacity to continue living on, despite all the abuse they take. Humiliated and insulted by how Ed understands him, Envy commits suicide by tearing out and destroying his own Philosopher's Stone. Meanwhile, the Armstrong siblings begin to gain the upper hand in their battle against Sloth; Izumi arrives in Central, allied with Briggs soldiers, to participate in the coup; and Hohenheim confronts Father alone.

The Armstrong siblings' and the Central forces' battle against Sloth rages on until Izumi appears and effortlessly pummels the homunculus, who is tossed and impaled on a spike by Alex and Sig, finally killing him. The Armstrongs and Curtises continue on around Central Command to wipe out the remaining mannequin soldiers, with Hohenheim and Father battling underground. With a majority of Central command captured, the Briggs forces are seemingly victorious until when King Bradley suddenly reappears, alive and unharmed, to overturn the coup and retake control of the country.

Hohenheim, who had managed to converse with all the souls within his Philosopher's Stone, had infused the souls into Father's body to destroy it from the inside. However, Father shows his true form and is able to survive outside of his container. Meanwhile, Bradley begins his attack on Central HQ and single-handedly takes on the resisting forces, as well as destroying Buccaneer's arm. As he reaches the main gate, he finds himself against Greed, and Bradley reveals his hidden Ultimate Eye to fight him. Buccaneer allows himself to be stabbed in order to take away Bradley's sword, though Bradley soon arms himself with daggers. Meanwhile, Falman and the remaining Briggs soldiers try to fend off the Central army, and Fu later arrives to assist Greed in facing Bradley.

Greed, unable to hurt Bradley, is pinned down during their fight, which forces Fu to fight Bradley alone. Fu attempts to perform a suicide attack to kill Bradley using explosives strapped to his chest, but Bradley defuses them and mortally wounds Fu. However, Buccaneer thrusts a sword through Fu's body before he falls and successfully stabs Bradley in the stomach, allowing Greed to further harm him, while Lan Fan arrives to witness her grandfather's death. Meanwhile, Ed's group encounters the doctor who created Bradley, and are pit against the numerous rejected Fuhrer candidates. The doctor then activates a transmutation circle, connected by the five research labs in Central, and absorbs Ed, Al, and Izumi.

Lin and Bradley's fight leaves them hanging over the side of the front gate, but Lin is saved by Lan Fan while Bradley falls into the moat below. As Buccaneer lays dying, he gives his final request to Lin to defend the front gate. Already distraught by Fu's death, Lin complies and draws upon the full power of Greed's Ultimate Shield to annihilate all Central forces before the gate. Underground, Ed, Izumi, and the unconscious Al reappear in Father's lair to find Hohenheim subdued. With four of the five human sacrifices, Father is left to wait for the fifth. The gold-toothed doctor in the levels above decides to use Roy as the candidate for the fifth sacrifice, has Riza's throat slit and tells Roy that he will only save her if he performs human transmutation.

Following Riza's eye signal, Roy refuses to perform a human transmutation. May arrives with Zampano, Jerso, and Darius and heals Riza's wound. However, Bradley and Pride also appear and force Roy to perform a human transmutation anyway, using the gold-toothed doctor as a sacrifice. Roy passes through the Gate of Truth and reappears in Father's lair with Pride, Father, and the other sacrifices, and finds he has lost his eyesight in exchange. Scar battles Bradley above, and May crashes through the ceiling of Father's lair to find Al unconscious. Al stands before the Gate to find his body, but despairs that he will be unable to use it to fight alongside the others because it is so frail. He promises to return for his body and goes through the Gate, regaining consciousness in Father's lair and completing Father's count for the five sacrifices.

Ed and Al battle against Pride while May tries to take on Father. Meanwhile, Ishbalans make plans within the city. In his fight against Bradley, Scar reveals a reconstruction transmutation circle from his brother's research now tattooed on his other arm. Just as Ed's group start to gain the upper hand and despite the arrival of Greed, Father grabs the four sacrifices and uses them, along with Hohenheim, for his transmutation circle, absorbing all the souls in Amestris. This opens a giant gate flat on the surface of the Earth from which rises a giant Father. Then another gate opens in the sky with a giant eye looking out which Father calls "God" and pulls towards him.

Everyone closest to the center of Father's nationwide transmutation circle, including Ed's group, survives to discover that Father has used the souls of over fifty million Amestrians to suppress God within a new, youthful body. Father neutralizes everyone's alchemy, but, before he can annihilate them, Hohenheim reveals his countermeasure: he had spent years traveling the country, placing fragments of his own Philosopher's Stone into the earth to use as foundation for returning the Amestrian souls to their bodies. The stone fragments are activated by the eclipse's umbra, and the souls are ripped from Father's body back into their original bodies, which weakens Father to the point of barely being able to suppress God anymore. The eclipse then lifts, blinding Bradley with sunlight and allowing Scar to kill him. Scar activates the nationwide alkahestry circle his brother and fellow Ishbalans had been preparing, which restores everyone else's alchemy at their greatest potential. Facing the full strength of his opponents' attacks in his unstable body, Father retreats aboveground to find more souls and replenish his stone supply. Ed remains behind to fight Pride while everyone else chases Father. Pride tries to steal Ed's body to replace his own unstable one, but Kimblee's soul reappears within him and taunts him while Ed enters his body and destroys it, reverting him to the form of a small fetus-like creature. Ed spares Pride's life and leaves to join his friends.

Hohenheim and the others stop Father from making Philosopher's stones, but as Ed rejoins them, Father spawns humans resembling the people of Xerxes before attacking with a powerful blast which takes out half the headquarters. They barely manage to survive the blast, but Al and Hohenheim take some heavy damage protecting the others. Before Father can kill Ed and Izumi, the Briggs soldiers, along with several of Ed's allies, join up to attack Father and use up his stone supply. Father lets down his barrier temporarily to try and absorb Greed's stone, giving Ed, Alex and Izumi the opportunity to damage him to the point of defending himself manually. As Father starts to lose control, he creates a blast which traps Ed's arm whilst his automail arm is destroyed. With Ed in danger, Al convinces May to help him perform a transmutation, trading his soul for the return of Ed's right arm. Al rejoins with his body on the other side and with his arm returned, Ed frees himself to unleash a series of blows on Father.

While being effortlessly pummeled, Father desperately tries to absorb Greed's Philosopher's Stone. Greed decides to part from Lin's body, and uses his carbonization ability to turn Father's body into weak charcoal. Father extinguishes Greed's soul, killing him, but Ed punches through Father's chest, releasing all the souls of the people of Xerxes and sending Father to the Gate of Truth where he is trapped for eternity. In the wake of Father's defeat, everyone mourns Al's sacrifice. Ed rejects using a Philosopher's Stone to bring him back to life, even after Hohenheim offers his final life as an apology for the pain Ed and Al were forced through. Ed ultimately decides to perform a human transmutation on himself, sacrificing his own Gate and his ability to use alchemy with it. As a reward for discovering he doesn't need to perform alchemy, Ed is allowed to bring Al back with him in his original body. As everyone recuperates from the battle, Hohenheim returns to Resembool and dies peacefully before Trisha's grave.

Deciding to help sort out Ishbalan policies, Roy is approached by Knox and Marcoh, who offer him a Philosopher's Stone to get his eyesight back, with Roy insisting it be used to fix Havoc's legs first. Olivier secretly rescues Scar so that he can assist Miles in rebuilding Ishbal. Having previously seen off Lin, who had promised to take care of May's clan among others once he becomes emperor, Ed and Al return to Risembool where an overjoyed Winry awaits them. Two years later, Grumman, who had become Fuhrer, visits Bradley's wife, who had been raising up Selim to be a compassionate child. Al decides to travel with Jerso and Zampano to Xing and other eastern countries to learn about alkahestry, whilst Ed learns what he can in the west, hoping to pool their research together. As Ed heads off, he and Winry finally express their love to each other using confusing terminology.