While Winry waits alone at Curtis’ butcher shop, Ed, Sig, and Izumi are apprehended by the State Army on the orders of Lt. Col. Archer. However, Ed and Curtis later escape from the clutches of the military, leaving the fake dolls behind.
Archer personally welcomes both Kimblee and Mr. Tucker back to the military, saying that Tucker can continue his research under his command. Archer then issues orders to wipe out the Devil’s Nest resistance, saying that with Tucker’s help, he can create more chimeras.
The battle in the sewers continues as the soldiers continue to kill members of Greed’s gang, including Bida. While Dolcetto faces the soldiers who are chasing them. Greed and the others are then confronted by Major Armstrong, who demands that Al be returned. As Lust and Gluttony observe the situation, Roa confronts Armstrong. After Armstrong transforms the top of his hammer into an artistic version of himself, Roa transforms into his chimerical form. After they both use their brute strength to injure each other, Roa reveals that he is also an Ishval Civil War vet like Armstrong. Just as reinforcements arrive for both the army and Greed’s men, Armstrong urges them to surrender. However, Roa punches a wall to make the gang escape and stops the army from following them. Greed reveals that he will make sure to later punish Kimblee and Tucker for their betrayal.
Lust and Gluttony confront Greed and the last of his gang in a nearby building. They demand that Greed dies or be sealed away, revealing that their master is very angry with him. Once Dolcetto frees Al, he and Roa decide to hold Lust and Gluttony back so Greed and Al can escape. They also encourage Al to take care of Martel, who is still in Al’s armor.
Ed, who is searching for Al alone, notices a disturbance towards Dante’s house; Greed separates from Al and Martel and requests that Martel stay in Al’s armor until the next day so she can at least survive, despite her objections.
After killing Roo and Dolcetto, Lust and Gluttony watch as Greed enters Dante’s house, with Lust noting that their work is done. Inside, Greed meets Lyra, who knows he was born in the house, and directs him to another room. As he enters, Greed slowly weakens and notices some bones on the table, which Lyra reveals are his bones.
Greed wants to know what Dante said to Lyra, whereupon Lyra shows him Dante’s body already on the floor, cut in half. Lyra then activates a transmutation, which Greed knows is beyond the capabilities of a low-level alchemist like Lyra. When Ed notices the transformation outside, Greed starts vomiting red rocks from his body. When Greed is barely out of the circle, Lyra disappears and Ed arrives. When Ed sees Dante’s body, he believes that Greed killed her, but Greed doesn’t care, and when Ed comes to save Al, Greed prepares to face Ed in battle despite his weakened state. Greed transforms into his full armor state and overpowers Ed, damaging his automail arm and knocking him to the ground. After remembering what he said earlier about killing him, Ed is able to perform alchemy on Greed’s arm and then turn the joints on the automail arm to turn it into flesh and bone. Ed reveals that the secret to Greed’s shield is that he raises the carbon in his body and proceeds to attack various points on Greed’s body, demanding where Al is. Ignoring Ed, Greed continues his offensive, trading blows until Ed transforms Greed’s chest to impale her with his automail sword, ending Greed.
As he is dying, Greed reveals that he has already released Al, and that while homunculi are born from failed human transmutation, when exposed to the remains of the human from which they were created, this particular homunculus weakens, its only weakness. . Greed encourages Ed to defeat the other homunculi, revealing that he wished to die instead of being resealed. Ed is saddened to see Greed leave and the skull Archer is holding also disintegrates. The next day, Al and Martel watch the sunrise before Martel leaves; once Al and Izumi meet up with Ed, the trio bury Greedo and Dante. Ed reveals to Izumi that he arrived too late to save Dante and has no idea where Lyra is. Later, the Elric brothers and Winry are ready to leave, and Ed reveals that they are heading to Ishbal, demanding that Izumi hide for a while in case the army comes after her. Once Ed admits that he won’t give up until he and Al get their bodies back, Izumi and Sig watch as the Elrics and Winry leave.