During the course of FMA's story, "Father" commands the other Homunculi and orchestrates the various conflicts like the Ishvalian war, plotting something involving a transmutation circle encircling the entirety of Amestris.

Spoiler

Most likely the very first Homunculus, "Father" met Hohenheim in the ancient country of Xerxes, where Hohenheim served as a servant in a laboratory. The Homunculus taught Hohenheim to read and perform alchemy, and was eventually brought before the king of Xerxes to give him immortality. After utilizing the life force of all of Xerxes' populace, Homunculus crafted himself a body akin to that of Hohenheim, and rendered them both immortal.