Ling, however, is overwhelmed by Father's presence, and feeling he is no different than his children for the way they treat humans prepares to engage him in battle. Father dismisses the Xingese prince and orders for Gluttony to devour him, much to Ed and Al's objection. Al quickly fills Ed in that Father is the one who created the Homunculi and realizing that Father is behind all the nefarious plots, a brief skirmish breaks out. After the objects from Ed and Al's transmutations have no effect on Father, Ed notices Father's ability to perform transmutation without even moving a single muscle as his own transmutations knock the three of them back. But the tide quickly turns when Father uses a transmutation which Scar, May Chang, and Hohenheim can sense that somehow cancels out the Elrics alchemy leaving them vulnerable and easily subdued by Envy. Ling is then overpowered by Gluttony who eats his sword. Surprised this is happening, Envy mentions to Ed that they never bothered to learn how they were able to gain their power in the first place, and makes it clear he never intended to fulfill his promise to Ed for freeing him from Gluttony's stomach. Having seen Ling in action has aroused Father's interest and he decides to turn him into a homunculus. Father reveals a hidden eye in his forehead and out comes a red liquid that Ed realizes is a Philosopher's Stone and Envy confirms to him that Father will turn Ling into a Homunculus. The Elrics become really worried when Envy also mentions the chances that Ling will die in the process of becoming a human-based Homunculus. Ed tries to use the gun Riza Hawkeye gave him, but Ling orders him to stand down as this is something he wants since this had been his mission to get a Philosopher's Stone.

After the fluid stone is absorbed through the cut on his face, Ling fights off it's effects and comes face to face with Greed. Ling willingly relinquishes his body, since he cannot waste the sacrifices he has made to obtain this power, especially after Lan Fan had to amputate her own arm for his sake. Ling's nature impresses the Homunculus and immediately takes over when the process is complete. Ed and Al are stunned to learn that the new Greed doesn't recognize them, showing no recollection of the events from Dublith and that Ling didn't resist being taken over. Suddenly, one of the guardian beasts enters the chamber, dead, killed by Scar. May Chang is feeling uneasy upon sensing Father and Scar can also tell that he is not a 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 upon hearing the word Fullmetal Alchemist, May asks where he is. However, May is heartbroken to learn that Edward is nothing like she had envisioned, and is actually the short kid that she met yesterday. Father has Gluttony attack Scar since Scar has been a hindrance to their plans, and despite being overconfident that Scar can't use alchemy, Gluttony is surprised that Scar's decomposition technique still works, which also surprises Father and Envy.

Accusing the Elrics of misleading her and kidnapping Xiao-Mei, May's emotional distress allows the Elrics to free themselves from Envy's grasp when she attacks Envy with alkahestry. But the brothers are still unable to use their alchemy, despite the fact that Scar and May are somehow using theirs without any trouble. Ed decides to turn Scar on the Homunculi, telling him the truth about Ishval and how Envy was responsible for the child shooting that started the conflict. An angry Scar decides to get more details out of Father about the truth and quickly takes down Gluttony again when he tries to attack Scar from behind. Scar begins to openly assault the lair, and Ed chases after Greed 2 in the hopes of getting through to Ling. While May is distracted by recognizing Ling from the Yao clan, Gluttony attacks her from behind and she runs away with Gluttony in pursuit. Scar quickly finds his decomposition technique has no effect on Father, who demands to know why it is still working. Scar barely dodges Father's couterattack that saves his life, but still leaves him injured, and it also distracts May causing her to be injured in the process. Al quickly saves May and rushes out of there with her and Xiao-Mei. During their escape through the sewers they are cut off by the guardian chimeras, and as an injured Scar arrives to help, Gluttony and Envy also arrive. Al asks Scar to flee with the injured May, where despite his problems with them and Winry, Al mentions that May comes first and the Homunculi cannot kill them due to being important sacrifices.

Scar refuses since he can't in his injured state and refuses to run. After Scar ignites the hydrogen, Envy quickly apprehends Alphonse, and notices that Scar had disappeared. Envy orders Gluttony to go after Scar, but discovers that Gluttony's stone has finally run out of power after dying numerous times. Meanwhile, Ed is fighting Greed 2, and briefly manages to get a reaction from Ling before also being captured once more. Father orders the brothers to be taken to Wrath above, while Edward tells Alphonse that even though Greed is in control, Ling is still inside his body.

After the credits, Father is shown watching over the dying Gluttony. Reaching inside and extracting his Philosopher's Stone, Father promises to recreate Gluttony with of his memories intact.