Father

The central antagonist of the manga and 2009 anime series. Father is an extremely powerful Homunculus identical in appearance to Hohenheim, excluding hairstyle, clothing, and lack of glasses. He is the creator of the Homunculi.

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 (though, Pride could have been referring to himself as the oldest of Father's children).

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 make the first Philosopher's Stone that 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, Lan 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 fighting each other. Father told Hohenheim, that he is about to become a part of him. Whether he plans to do it only to Hohenheim or to every other candidate to the sacrifice is still not known. After a short battle, he manages to stab Hohenheim and claim his Philosopher's Stone but the thousands of restless souls composing it manage to destroy his human body from the inside.

Unfortunately, this isn't enough to kill Father as his original Homunculus form, now fully evolved (looking like a big human shaped version of his former self with a grinning mouth and multiple eyes) emerges from his container, absorbs it with the Philosopher's Stones it still contained and restarts the fight.

Appearance and Abilities
Due to his imitation of Hohenheim's body in Xerxes he looks identical in appearance to Hohenheim, excluding hairstyle, clothing, and lack of glasses. He is normally seen in the cavity beneath Central in which he and the Homunculi reside, sitting on a stone or cement 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, but it is implied that they are used to supply the country with souls from his Philosopher's Stone so that Amestrian-style alchemy can be performed, especially with Envy's statement to Edward after Father performs his alchemy disabling technique and when May states that the presence of souls beneath the ground are stronger around Father's chamber.

During his battle with Van Hohenheim, father left his body (swallowing the empty moult-like shell left behind afterwards) to expose his new evolved form

Father's body is composed of a huge number of Philosopher's stones, made from half the souls of the people of Xerxes. Due to this, he is able to perform alchemy without drawing a transmutation circle or clapping his hands together. He can also ignore Equivalent Exchange. This is demonstrated in Chapter 54 when he effortlessly repels the Elric brothers' attacks while literally standing still.

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, and attempts to steal Hohenheim's Philosopher's Stone during their battle.

Father also has also been shown to be able to prevent alchemists from performing Amestrian alchemy as seen when he nullifies Ed's ability to use the art. It is later stated that no alchemists within a large part of Central could use their alchemy either. It is unknown how he did this, but it is likely he prevented them from drawing energy from the earth as Amestrian alchemy requires. 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 on Xing style and Mei is a native of the 12 Countries of Xing). This seems to startle Father a bit.