Shortly after Gluttony and Al arrive at Father's lair, Gluttony's stomach opens up, and Envy, Ling, and Ed emerge. Al is ecstatic to see his brother again, but what really gets Ed's attention is how Father looks exactly like Hohenheim. Father is surprised to learn that Hohenheim actually had children, and when he sees that both brothers are injured, he repairs Al's armor and heals Ed with alchemy because the two are important human resources. As a result, the brothers realize that Father's alchemy is special and doesn't obey the rules of equivalent exchange. Father, however, has no need for Ling and wants Gluttony to eat him. His views on the insignificance of humans in general angers Ed into attacking him, but Father easily counters everything the brothers and Ling throw at him. Feeling that this is a waste of time, Father takes away Ed and Al's alchemy with one step of his foot, making them powerless against Envy and Gluttony. He's changed his mind about Ling though and decides to make him into a Homunculus by dropping a Philosopher's Stone into his body. Much to Ed and Al's surprise, Ling is willing to go through with this, and he soon finds himself face-to-face with Greed. Ling's desire for absolute power leads to him giving up his body, and so Greed takes over, though this Greed has no memories of the previous Greed.
Greed's appearance is interrupted by the arrival of Scar and May Chang to the lair. Though initially fearful of Father, May Chang is happy to be reunited with Shao May, and she's shocked to see what Edward Elric is really like. To everyone's surprise, both Scar and May Chang are still able to use their alchemy, and Ed decides to use this to his advantage by telling Scar that Envy was responsible for what happened to his people. This succeeds in turning Scar against Father and the Homunculus, but even Scar can't seem to harm Father and barely escapes with his life. Al meanwhile saves May Chang from Gluttony and escapes as well, but he and Scar get sandwiched between the Chimera horde and the Homunculus. Because he knows that he's important to Father, Al decides to help Scar and May Chang get away even though that means he himself will get caught, and Gluttony can't give chase because he's got no more regenerative powers since he's died so much. Ed meanwhile fights Greed, and even though he lands a punch after invoking Ling's country and Lan Fan, Greed is eventually able to restrain him, and Father orders that the brothers be taken to Wrath. Despite the fact that Greed appears to have completely taken control of Ling's body, Ed still believes that Ling is somewhere inside. In the aftermath, Father removes a Philosopher's Stone from Gluttony and decides to remake him.