Episode 44: Hohenheim of Light (2003 series)

With the mastermind behind the seven sins organizing a plan to capture the boys as well, Ed and Al must convince Mustang's faction that the Fuhrer is not what he seems. The strange reappearance of their father only complicates things further, as we learn he has his own score to settle.. one that goes to the root of this entire conspiracy.

Full Synopsis
Lyra and Rosé descend a secret staircase in an old church. At the bottom, the Homunculi Lust, Sloth, Wrath and Gluttony are awaiting their arrival. Edward and Alphonse explain to Colonel Mustang that they ran because Führer King Bradley is a Homunculus (Pride) and therefore part of the conspiracy over the Philosopher's Stone. They still keep Al's new status as the stone a secret, however. Ed and Al learn of the reappearance of their father upon their return to the Rockbell house. Al is excited to see him, but Ed is angry enough to deck Hohenheim with one punch. Hohenheim disappears early the next morning after overhearing Ed describe Lyra as wearing the same obnoxious perfume he has smelled on his father, and Al's relief that Lyra had escaped Dante's house safely (after Dante's apparent murder by Greed). Hohenheim arrives at the same entryway where the Homunculi were waiting for Lyra. Hohenheim recognizes her immediately as Dante, her soul now residing in Lyra's body. Dante has been controlling the Homunculi all along. Hohenheim offers to explain why his body and Dante's new body are decaying in exchange for a promise to leave his sons alone. Edward assigns himself a grisly task--desecrating his mother's grave to obtain a piece of her corpse to use as a weapon against Sloth after learning what happened to Hughes.

Trivia

 * At the beginning of the episode, Lyra discusses a religion that is now extinct in the world of Amestris. It is strongly implied that said religion was Christianity, especially given Izumi's comment in a later episode that the dating system based on the birth of Christ was once used by an "ancient religion".