I've been working for sometime now on a general theory of where Father came from, his history and what he is trying to do, here are my compiled thoughts on the subject so far. Please read and discuss . . .
In the Ancient Empire of Xerxes, there was an alchemist to the Emperor. Legends told of the Doors of Truth, a great gate where entities of unimaginable intelligence exists, holding the True knowledge of alchemy.
The Emperor’s Alchemist use his abilities to channel the power of the Gate and draw part of the entity that exists there into this world, mixing it with the blood of his slave Number 23 so it could sustain itself in this world. It went by the name “Homunculus”. However it could only exist as a shadowy spirit in a container, if it was to leave it glass prison, it would die.
Homunculus befriended the slave, perhaps feeling bonded by blood, named him Van Hohenheim and used his vast knowledge to teach him to read, write and how to perform alchemy. When Hohenheim grew more proficient, his Master noticed and allowed him to aid in more difficult and alchemic tasks.
Soon enough the Emperor called on Homunculus for his great knowledge and asked him how to become immortal. Homunculus saw his opportunity for freedom and instructed the Emperor to construct a Transmutation Circle around the entirety of Xerxes and create bloodshed in certain points on the circle.
Once completed they gathered, the circle was activated with Homunculus and Hohenheim at the true centre and all in Xerxes bar them were sacrificed to create the Philosopher’s Stone, perhaps the first Stone. Being a homunculus with no form, he could not perform alchemy, so he manipulated the Emperor to this moment so he could open the Gate and constructed a form using half the souls of Xerxes in Hohenheim’s likeness to occupy granting him a body, and using the soul’s power he could now perform alchemic feats himself.
The other half of the souls of Xerxes Homunculus gives to Hohenheim as thanks; his body too becomes a Philosopher’s Stone, immortal, powered by the souls of Xerxes. Hohenheim is devastated at what he helped do, presumably they part ways at this point.
Van Hohenheim, with his newly powered Philosopher’s Stone body, travels East to a land called Xing. Here he mixes the true alchemy of Xerxes with their arts of healing, primitive alchemy and methods to gain immortality to form the alchemy of Rentanjutsu that the Xingese now use. (A legend that becomes known as the Philosopher of the West) He leaves at some point to travel to Amestris; tiring of his immortality he settles down and starts a family.
Homunculus, who at some stage changes his name to Father, travels west and teaches the people he meets an alchemy that taps into the power of the Souls of Xerxes Father has contained in his body, which becomes known as Renkinjutsu. (A legend that becomes known as the Sage of the East) The Military State of Amestris forms, with a puppet government controlled by Father and begins to annex all the territory nearby, with perfectly precisioned battles to form a transmutation circle much like in Ancient Xerxes.
He creates more Homunculi as he once was to carry out his bidding and ensure his plans come into fruition. They are created one of two ways that is known so far, the standard Homunculus is created from a Philosopher’s Stone which becomes their core. They cannot perform alchemy, but have incredible and varying powers but are limited as once the souls of their Philosopher’s Stone are exhausted they can truly die. The other type of Homunculus is created by a Philosopher’s Stone being forced into a human’s body, an agonising process which usually just kills the subject. If successful, the Stone takes over the person’s body, becoming a Homunculus. Some part of the human that once existed still exists inside the Homunculus, but is mostly taken over by the raging personality of the Stone. Presumably the die the same way as a normal Homunculus, when the Stone’s souls are exhausted, however none of these type of Homunculi have been killed as of yet.
Father appears to be planning to use the entire country of Amestris to open the Gate as he once did in Xerxes, but what he plans to achieve by doing this is yet unknown. He apparently requires human sacrifices, alchemists who have seen the gate themselves by performing failed human transmutations. What purpose these sacrifices are to serve is also unknown. Perhaps he could be planning to draw the remainder of the shadow entity from the Gate into the FMA world.
Note: Van Hohenheim being the Philosopher of the West has caused a fair bit of discussion and disagreement. However, I am certain that he has to be:
1: There has been talk of a third Hoho lookalike that is the Philosopher of the West. This is rubbish. The only reason a third lookalike has been considered is because people rejected the idea of Hoho being the PotW and there had to be someone else, so a 3rd Hoho was created, but doesn't exist.
2: PotW came from Xerxes. Father went to Amestris and taught them so it can't of been him, especially since he would then be able to recognise Xingese alchemy. Considering that the entirety of Xerxes was annihilated except for Father and Hoho, there is only one other person with great alchemic power from Xerxes: Van Hohenheim.
3: Read the Chapter where Ed goes to the ruins of Xerxes to meet Maria Ross. Ran Fan explains the legend and says the PotW mixed the alchemy of Xerxes with their primitive alchemy and medicinal knowledge to create the Rentanjutsu that they use now. They already had some alchemic knowledge, Hoho merely adapted their knowledge and his together, forming a new alchemy which Father could not recognise.
4: In Chapter 75, Hoho uses Xing alchemy to heal Izumi Curtis, so he has obviously been in Xing and knows their alchemy.
I have yet to see a convincing argument as to why Van Hohenheim could not be the Philosopher of the West.
Right . . . please have a look and tell me your thoughts.