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, lack of glasses, and the addtion of a few wrinkles. This is due to the fact that when he gained a body, he decided to copy Hohenheim, since Hohenheim was his friend and having Hoenheim`s blood made it easier to assume his form. He is the creator and leader of the Homunculi.
Due to his imitation of Hohenheim's body in Xerxes, Father's first form looks identical in appearance to Hohenheim, excluding hairstyle, clothing, and lack of glasses. Hohenheim has referred to this form as nothing more than a human-like husk his Homunculus enemy has fashioned for himself to hide his true appearance. He is normally seen in the cavity beneath Central in which he and the Homunculi reside, sitting on a stone or cement throne with numerous pipes leading to it. The throne itself also has a physical connection to him, which can be unattached from him via pipes directly protruding from his spine. He uses the pipes to spread the Philosipher's Stone beneath Amestris. The purpose of spreading the Philosopher's Stone under the nation is to act as a barrier between the tectonic energy of earth's crust (where Amestrian Alechemy gets its energy from) so he can stop others from using Alchemy when he needs to. This is later countered by the "Reverse Transmutation Circle" that Scar's brother had figured out by combing Alkahestry and Alchemy practices. Xing-style alchemy, or Alkahestry was unaffected by this (since Alkahestry gains energy from earth's chi instead), as seen when Scar and May continue using their alchemy against him (Scar's alchemy is based on Xing-style and Mei is a native of the 12 Countries of Xing).
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. It is unknown why Father alone is capable of using alchemy out of the Homunculi. His first six Homunculi "children" were also created directly from his body using Philosopher's Stones as their cores; however, Wrath and the second Greed had the Philosopher's Stone injected into their original human 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.
In chapter 90, Edward Elric, Van Hohenheim, Scar, Lan Fan and the Chimeras are invading his lair with plans to finally kill him. In chapter 91, Only Hohenheim manages to reach him, Father told Hohenheim, that he is about to become a part of him. After a short battle, he manages to stab Hohenheim and claim his Philosopher's Stone but the souls composing it manage to destroy his humanoid 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. He defeated Hohenheim, absorbing him into his body and later greeted Izumi Curtis and the Elric brothers, who did not recognize him at first.
In chapter 108, Father is seen on the verge of dying and wonders how a mere human is defeating him. As he struggles to keep in God, he rushes toward Greed-Ling and claims the Philosopher's Stone. Although Ling endeavors to keep Greed, he fails and Greed is absorbed by Father. Greed takes this opportunity to start destroying Father's body by using his power of carbonization to make Father's skin as weak as charcoal. Enraged that his own son would rebel against him to the end, Father destroys Greed's soul. But due to Greed's efforts, his skin is still weaker than charcoal, and Edward uses this opportunity to punch a hole though Father's chest. No longer able to contain God, Father collapses in on himself and is sent to the Gate of Truth.Father, now in his original form, appears before the Gate and asks God why he didn't become one with him, to which God replies, "It's because you did not believe in me." When Father searches for the origin of the voice, he is surprised to see God appear before him. Taking on the appearance of Father's own personal Truth (a white ball with a faint shadow around it), God berates Father for trying to take the power of someone greater than him. Father claims that he wanted all the knowledge in the world and that he wanted to know what God knew. God mocks him, saying that taking the power of God didn't make him God, but rather a cunning thief. God remarks that Father never grew up and reminds him what he said about Truth to his opponents: it gives us suffering so that we don't become boastful and proud. God tells Father that he'll know that fact first hand as the Gates open while Father cries out, "No.....I don't want to go back there!" Ultimately, Father is sucked into the Gate and once again becomes part of the endless abyss within.