Gluttony and Alphonse arrive at the father’s underground lair, a man Al immediately notices bears a striking resemblance to his father, Hohenheim. Suddenly, Gluttony is overcome with seizures as his false gate opens and Envy tumbles out of his stomach along with Edward and Ling. Alphonse is delighted to be reunited with Ed, to which Ed apologizes, while Xiao-Mei freezes when she looks at her father. Ed and Al’s reunion is interrupted when their father starts watching them and identifies them as the Elric brothers. Despite Ed believing himself to be their father, Hohenheim, he quickly realizes that the father is not actually him. The father is surprised by this connection when Ed states that Hohenheim is their father, and the father also learns from Ed that their surname Elric is actually from their mother instead of their father. Admitting that he has no idea where his father is, Ed, noticing their injuries, puts his left hand back into Al’s armor and heals Ed’s broken left arm and bruised ribs. Ed and Al are surprised because this completely ignores Equivalent Exchange.
However, Ling is overwhelmed by his father’s presence and sensing that he is no different from his children in how they treat people, he prepares to join the battle. Father releases Prince Xinges and orders Gluttony to eat him, to which Ed and Al object. Al quickly fills in on Ed that the father is the one who created the Homunculi, and a brief skirmish ensues when he realizes that the father is behind all the nefarious plots. After the items from Ed and Al’s transmutations have no effect on the father, Ed notices the father’s ability to perform the transmutation without moving a muscle as his own transmutation knocks all three of them back. But the tide quickly turns when the father uses a transmutation, which Scar, May, and Hohenheim sense somehow disrupts the Elric’s alchemy, leaving them vulnerable and easily subject to envy. Ling is then overcome by Gluttony, which eats his sword. Surprised that this is happening, Envy mentions to Ed that they never bothered to learn how they were able to gain their power, and makes it clear that he never intended to fulfill his promise to Ed for freeing him from Gluttony. Seeing the Ling in action piqued his father’s interest, and he decided to turn it into a homunculus. The father reveals a hidden eye in his forehead and a red liquid flows from it, which Ed realizes is the Philosopher’s Stone, and Envy confirms to him that the father will turn Ling into a Homunculus. The Elrics get really worried when Envy also mentions the likelihood of Ling dying in the process of becoming a human-based Homunculus. Ed tries to use the weapon that Lt. Hawkeye gave him, but Ling orders him to stand up because it’s something he wants since it was his mission to get the Philosopher’s Stone.
After the liquid stone is absorbed by the cut on his face, Ling fights its effects and faces Greed. Ling willingly gives up his body because he cannot waste the sacrifices he made to gain this power, especially after Lan Fan had to amputate her arm for him. Ling’s nature impresses the Homunculus and he immediately takes over when the process is complete. Ed and Al are stunned to discover that the new Greed doesn’t recognize them, doesn’t remember the events of Dublith, and that Ling didn’t resist taking them over. Suddenly, one of the guardian beasts enters the chamber, dead, killed by Scar. May Chang feels uneasy when she feels that the father and Scar can also tell that he is not human. Xiao-Mei immediately returns to May and May is happy to see her again. Scar is relieved that the Elrics are not allied with the Homunculus, and when May hears the word Fullmetal Alchemist, he asks where he is. However, May is heartbroken to discover that Edward is nothing like she imagined and is in fact the little child she met yesterday. Father has Gluttony attack Scar because Scar was an obstacle to their plans, and despite being too sure that Scar can’t use alchemy, Gluttony is surprised that Scar’s decomposition technique still works, surprising Father and Envy as well.
Accusing the Elrics of tricking her into kidnapping Xiao-Mei, Maya’s emotional turmoil allows the Elrics to break free from Envy’s grip as she attacks Envy with alkahestria. But the brothers still can’t use their alchemy, even though Scar and May somehow use theirs without a problem. Ed decides to turn Scar on the Homunculi and tell him the truth about Ishval and how Envy was responsible for shooting the child that started the conflict. Angered, Scar decides to get more details about the truth from his father and quickly defeats Gluttony again when he tries to attack Scar from behind. Scar starts openly attacking the lair, and Ed chases after Greed 2, hoping to get to Ling. While May is distracted by recognizing Ling from the Yao Clan, Gluttony attacks her from behind and she escapes with Gluttony. Scar quickly discovers that his decomposition technique has no effect on his father, who demands to know why it still works. Scar narrowly avoids Father’s counterattack, which saves his life but still leaves him injured, and also distracts May, causing her to be injured in the process. Al quickly rescues May and rushes out of there with her and Xiao-Mei. As they escape through the sewers, they are cut off by guardian chimeras, and when an injured Scar arrives to help, so do Gluttony and Envy. Al asks Scar to escape with the injured May, where despite his issues with Scar murdering Winry’s parents in a blind rage, Al mentions that May comes first and the Homunculi cannot kill him or Ed as they are important victims.
Scar refuses because in his injured state he cannot and refuses to run. After Scar ignites the hydrogen, Envy quickly restrains Alphonse and notices that Scar has disappeared. Envy orders Gluttony to go after Scar, only to discover that Gluttony’s stone has finally run out of power after dying many times. Meanwhile, Ed battles Greed 2 and briefly manages to get a reaction from Ling before he is also recaptured. Father orders the brothers to be taken to the Wrath above, while Edward tells Alphonse that even though Greed is under control, Ling is still in his body.
After the credits, the father is shown watching over the dying Gluttony. Father reaches in and takes out his Philosopher’s Stone, promising to recreate Gluttony with his memories intact.