Father

The central antagonist of the manga series. Father is an extremely powerful Homunculus identical in apperance to Hohenheim, excluding hairstyle, clothing, and lack of glasses. He is the creator of the Homunculi, and a manga-exclusive character.

Pre-Amestris
The character Father was originally a sentient shadowy substance (Who at times could form eyes and a wide grin), which was created in a flask during the time of the ancient civilization of Xerxes, by the Alchemist to the king of Xerxes who used the blood of his slave, Number 23. Contrary to Pride's statement, Father could actually be considered the first Homunculus.

Being a homunculus with no form, Father was unable to perform any alchemy of his own, so he befriended Slave 23, taught him to read, write and perform alchemy and named him Van Hohenheim. The king called on Father (currently going by the name "Homunculus") to give him the secrets to become immortal. Father used this opportunity and instructed the king to construct a giant transmutation circle out of the kingdom, creating bloodshed at specific nodes of the circle.

He then manipulated the event so he and Van Hohenheim were standing at the true center of the circle, so once it was activated, every soul in Xerxes besides Father and Hohenheim were sacrificed to possibly the first Philosopher's Stone was created.

Father used this power to open the Doors of Truth and created himself and Van Hohenheim new immortal bodies, living embodiments of the Philosopher's Stone with the millions of souls of Xerxes split between them as their power.

Horrified at what he aided in doing, Van Hohenheim parted ways with Father.

The Sage of the East and the Founding of Amestris
After the destruction of Xerxes, Father made his way west where a small group of people were attempting to thrive. Father took these people under his wing and taught them alchemy, however he did not teach them true alchemy, but an alchemy that took its energy directly from the souls of Xerxes contained in Father himself.

From this point the people formed into a powerful military state called Amestris, a puppet government secretly run by Father. Amestris begins to rise in power and annexes all nearby land, eventually branching out to form yet another giant transmutation circle, with all skirmishes and bloodshed involving the Amestrian military taking place at the important nodes of the circle.

Father plans to use Amestris just as he did Xerxes, to create a huge philosopher's stone; however, he seems to require alchemists that have opened the Gate as human sacrifices. In Chapter 73, he is shown moving five pieces around a transmutation circle; two being the Elric brothers, another being Izumi Curtis, and the fourth being Hohenheim. It is implied that he needs another alchemist to open the Gate. It is not known what he needs the human sacrifices for.

In chapter 90, Edward Elric, Hohenheim, Scar, Ran Fan and the Chimeras are invading his lair and plans to kill him. In chapter 91, Only Hohenheim managed to reach him and the two living Philosopher's Stones are about to fight each other. Father told Hohenheim, that he is about to become a part of him. Wether he plans to do it only to Hohenheim or to every other candidates to the sacrifice is still not known.

Appearance and Abilities
Due to his imitation of Hohenheim's body in Xerxes he looks identical in apperance to Hohenheim, excluding hairstyle, clothing, and lack of glasses. He is normally seen tn the cavity beneath Central in which he and the Homunculi reside, sitting on a stone chair with numerous pipes leading to it. The chair also has a physical connection to him, which can be unattached from him. The purpose of the pipes is unknown.

Father's body is composed of a huge number of Philosopher's stones, made from the souls of the people of Xerxes. Due to this, he is able to perform alchemy with hardly any effort and is able to completely ignore Equivalent Exchange, as shown in Chapter 54 when he effortlessly repels the Elric brothers' attacks.

The Homunculi were created by him through with the Philosopher's Stone; however, Wrath and the second Greed had the Philosopher's Stone injected into their bloodstream. Father is also able to remove these stones without much effort, as in Chapter 56, when he takes the nearly depleted Stone from Gluttony's body.

Father also has the ability to cancel out the power of Amestrian alchemy, shown when he nullifies Ed's ability to use the art. It is later stated that no alchemists with a large part of Central could use their alchemy either. Xing style alchemy is unaffected by this attack, as seen when Scar and Mei continue using their alchemy against Envy (Scar's alchemy is based off of Xing style and Mei is a native of Xing). This seems to startle father a bit.