Van Hohenheim

Ed and Al's mysterious father, who disappears a few years after they are born

In the Manga
In the Ancient Empire of Xerxes, an alchemist of the Emperor created a Homunculus in his laboratory using the blood of his slave No. 23. The homunculus was a vastly intelligent being with great alchemic knowledge but could only exist in his glass jar prison.

Homunculus befriended the slave, perhaps feeling bonded by blood, named him Van Hohenheim and taught 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 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.