Father

ORIGINS AND HISTORY
The character who would become known as Father was originally a sentient shadowy substance created in a flask during the time of the civilization Xerxes, partially from the blood of one of the alchemist' slaves. Originally named 'Homunculus,' it is not entirely clear as to why he was created, although a scene where he is brought before the king of Xerxes to be asked the secret of immortality suggests that he was created to acquire knowledge.
Homunculus was attracted to the slave who had given him blood, number twenty-two, because it was his blood that created him. Out of gratitude for helping to create him, Homunculus gave the slave a name, 'Van Hohenheim,' and started teaching him how to read and write and perform alchemy, which alleviated him from the position of a slave. The two became close friends, with Hohenheim being grateful for the life that Homunculus had given him, and the latter considering the former to be like a father.
Desiring to be able to leave his flask, when asked how to achieve immortality, Homunculus manipulates the king to create a country sized transmutation circle and massacres as 'crests of blood' needed, but unbeknownst to the king or anyone else the true centre of the circle where the one standing is unharmed and who receives the gain was where Hohenheim was standing, holding Homunculus. Using the souls of the entire country of Xerxes to create a Philosopher's Stone, and using Hohenheim's body as the sacrifice or 'passage fee' required to 'open the gate' and gain 'true knowledge,' Homunculus creates for himself a body from the information that was in Hohenheim's blood that was part of Homunculus and divided the souls of Xerxes between him and his 'blood' kin, effectively turning himself and Hohenheim into Philosopher's Stones.
Amestrian legend holds that their alchemy was taught by the 'Sage of the East,' who hailed from the fallen civilization of Xerxes. Due to the fact that he seems to know how Amestrian alchemy operates by rendering it useless during his battle with the Elric Brothers, it is implied that Father is the 'Sage of the East.'
CHARACTER OUTLINE
Father is a cold and pragmatic person who loathes treachery of his plans. He considers himself an existence far beyond human, comparing them to insects, and anyone who isn't useful in his plans is considered expendable. His goal appears to be to create the perfect Philosopher's Stone and to 'open the gate' (i.e. to a different dimension that contains all knowledge), by using all of the citizens of Amestris. His plan also involves the use of 'human sacrifices' to open the gate, those referred to as such have been alchemists, with those who have 'opened the gate' before (Elric Brothers, Van Hohenheim and Izumi Curtis) as 'confirmed sacrifices.' Because 'opening the gate' requires a sacrifice or 'transferral fee,' it is implied that Father intends to sacrifice the physical bodies of those who have 'opened the gate' as the transferral fee, possibly to acquire all knowledge from it as the more that is sacrificed gives more knowledge. However, there is very likely more to the plan, as Envy has let on several times to characters who have attempted to figure it out ("Are you planning to create a philosopher stone using this country?!" "HA! That's close!"). It is revealed that he created the country of Amestris solely for the sake of his master plan, and is directly responsible for all of the deliberately bloody and chaotic wars of expansion that it has waged.
POWERS
Father has the power to nullify all alchemic processes within a large radius of himself, rendering any alchemic reaction to be impossible. However, this ability does not affect Xingese alchemy. The reason for this is that the two types of alchemy use different power sources. Xingese alchemy uses the power that "flows from mountain into underground, nourishing land as it passed by", whereas Amestrinian alchemy relies on tectonic energy from the Earth's crust. He can perform alchemy purely through thought, with no movement whatsoever, and that he can transmute with any part of his body, not merely his hands as with most other alchemists. A third eye can appear in his forehead, which secreted the Philosopher's Stone that was the Homunculus Greed's nucleus (This suggests that Wrath, who like the post-Ling Greed is a human based Homunculus, was produced in a similar way). Because he is essentially a Philosopher's Stone, Father is capable of 'violating' the law of Equivalent Exchange, as demonstrated when he replaces Al's missing hand without having to rely on the material from his body and make his armour thinner.
PLOT SUMMARY
In chapter 73, it's revealed that Father needs five human sacrifices to 'open the gate,' all of whom have 'opened' it before. He is shown placing four pieces, representing Edward and Alphonse Elric, Van Hohenheim, and Izumi Curtis (all people who have seen the Doors) at four corners of a transmutation circle. He has yet to find one to fill up this fifth slot, however, it is implied that he intends to use a different alchemist to open the gate beforehand (such as Marcoh or Mustang).
In chapters 74-75, during one of Father's rare sleeping periods, he dreams of his past. It is revealed that he met Van Hohenheim when Van was a boy slave in a laboratory. Father appeared as a small ball of shadows (resembling the ones Pride controls and those inside the Doors of Truth) inside a round flask. The conversation revealed that Van's blood had been extracted by his owner and used to create the being who would later become Father. When Van asks the ball what its name is, he tells him to call him "Homunculus". Over time Homunculus educates Van in reading, writing and basic alchemy. Some time later, the king of Xerxes summons Father and his Master to the palace and wants immortality. Homunculus convinces the king to dig trenches around the country in the shape of a transmutation circle. When the circle is activated, the country and people are consumed and Homunculus uses Hohenheim's body as the 'transferance fee' to 'open the gate'. He also uses the 'information' from the blood that came from Hohenheim body to create a new 'container' for himself that resembled Hoheheim. He refers to Van as his 'blood kin'. As a gift for helping him, Homunculus made Hohenheim immortal by rebuilding his body with half the souls of the population of Xerxes. The other half Homunculus used to create his own body. In addition, Father is most probably the legendary sage of the east that taught Amestrians Alchemy. This is because he was created in Xerxes, west of Xing and east of Amestris, as well as what would seem to be the birthplace of all Alchemy. Evidence shows that Amestrian Alchemy is the creation of father so it makes sense that he is the sage of the east. By contrast Hohenheim is likely the Sage of the west from Xing legend. He has been shown to be a master of Xing alchemy and was also from Xerxes and in chapter 76 May-chan said that the sage of the west had gold hair and gold eyes just like Hohenheim and the Elric brothers just as Winry pointed out.
Father's plans are very near to fruition, because in chapter 78 Sloth eventually finishes to build the tunnel underneath Amestris. Nonetheless, an encounter between Van Hohenheim and Pride in the caves underneath Lior seems to concern him.