The Dwarf in the Flask: Homunculus, referred to as "Father" by his "children", the other homunculi, is the central antagonist of the Fullmetal Alchemist manga and 2009 anime series. He is the oldest Homunculus and the progenitor of the Homunculi, creating them directly or indirectly. Arrogant and self-righteous, he deems only power over and ownership of the world, "perfect goodness and being", and "divine order" worthy of his attention, and he seeks to become absolutely "superior" to the human race. One of his outward looks bears a striking resemblance to Van Hohenheim.
"Father" was created from the essence of the Eye, and thus Father's shadowy actual form greatly resembles the Eye. "Father" inherited much knowledge from the Eye, and, when it comes to amount, only those of the Eye and Truth exceed his knowledge.
While it is never fully explored, the being that would later call itself Father was originally a part of the existence within the Gate. Using the blood of his slave Number 23, the Alchemist to the King of Xerxesmanaged to contain a small portion of the knowledge and life of the Gate within a flask, capable of existing in the physical realm. Named simply "Dwarf in the Flask" or "Homunculus" by the people of Xerxes, this sentient creature contained a vast amount of knowledge, the most important and influential being the skills that would become standard alchemy.
The Dwarf in the Flask was unable to perform any alchemy of his own. Furthermore, though the flask was the only thing that keeps him alive, Homunculus desired to exist outside it. To that end, he befriended Slave 23 out of similar circumstances as slaves to their respective plights, in turn naming the lad Van Hohenheim and educating him to win his freedom as an act of thanks for his hand in creating him.
However, Homunculus grew envious of the human race, jealous of their mutual emotional support for each other whilst he grew lonely, being only one of his kind. Losing sight of his own unique, supreme, and special gifts and talents, Homunculus lost much of his self-confidence, and this low self-esteem caused him to fill himself up with hubris and a desire to become a being superior to even God himself.
Years later, the King of Xerxes finally revealed the use for Homunculus; he wanted to call upon him to give the secrets of immortality. Homunculus used this opportunity and instructed the king to construct a giant transmutation circle out of the kingdom, creating bloodshed at specific nodes of the circle. He then manipulated the event so he and Hohenheim were standing at the true center of the circle, so once it was activated, every soul in Xerxes besides himself and Hohenheim were sacrificed to make what was possibly the first Philosopher's Stone ever created.
Homunculus used this power to open the Gate of Truth and created new, immortal bodies for himself and Hohenheim, living embodiments of the Philosopher's Stone with the hundreds of thousands of souls of Xerxes split between them as their power. Horrified at his role as an unwilling partner in this horrific act, Hohenheim parted ways with Homunculus.
After the destruction of Xerxes, Homunculus made his way to find another inhabited place. Finding such a patch of land, he took the small group of people thriving there and taught them alchemy, becoming known as the "Philosopher of the East". However, to ensure his teachings would not be used against him, he placed himself under what would become Central Command and used himself as a buffer against tectonic energy so alchemists would actually use energy derived from the souls of Xerxes contained within himself. At some point, he began using those same souls to create his Homunculi offspring and accordingly started going by the name "Father".
From this point, the people formed the powerful military state of Amestris, a puppet government secretly run by Father. Amestris begins to rise in power and annexes all nearby land, eventually branching out to form yet another giant transmutation circle, with all skirmishes and bloodshed involving the Amestrian military taking place at the important nodes of the circle. While Father's scheme was to repeat his actions at Xerxes to create another Philosopher's Stone, he now requires an eclipse to become a "perfect being", and five alchemists that had opened the Gate as human sacrifices.
Throughout the first half of the story, Father is mostly seen sitting on a stone throne with many pipes leading into it. He is properly introduced when Wrath captures Greed and brings him to Father's underground lair. After his offer to the Homunculus was turned down, Father had Greed boiled in a tub of liquid which decomposes his body into his core Philosopher's Stone. The Stone, now in a liquid state and containing Greed's soul, is then consumed by Father.
Father's full identity is revealed when Gluttony brings Alphonse into the Homunculi's lair, prior to Gluttony's body tearing apart as Envy, Edward and Ling Yao emerge from Gluttony's stomach. When the Elrics recognize his face, Father admits his amazement that Edward and Alphonse are Hohenheim's children, before healing Edward's wounds and restoring Alphonse's missing arm. Having no use for Ling, however, Father orders Gluttony and Envy to kill him. Edward pleads for him to spare Ling, but Father makes it clear that he does not care for anyone not a part of his plan. Edward and Alphonse use their alchemy to attack Father, with no avail; Father is entirely unharmed by their attacks before he merely stomps his foot to seal off all alchemy in Central.
However, entering Father's lair at the same moment, Scar and May Chang astonish Father with their own counterattacks, unaffected by his alchemic lock-out with their own unique forms of alchemy. However, even point-blank, Scar's alchemy is unable to harm Father. Scar and May are overwhelmed while Envy captures the Elrics. Meanwhile, Father too easily defeats Ling and then takes the liquefied stone, in which Greed is contained, and merges it with Ling, stating that he could have use for another pawn after all. Ling then becomes the new Greed and Father has the Elrics taken to the surface before tending to the injured Gluttony. From there on, Father is mostly seen sitting on his throne, musing over his plan and conversing with the military high command.
When the Promised Day begins, Edward, Hohenheim, Scar, Lan Fanand the Chimera invaded his lair with plans to kill him for good by destroying his shell. However, only Hohenheim manages to reach him as the two do battle. But when it seems Father has won when he manages to stab Hohenheim, he learns all too late that Hohenheim managed to work with the souls within his Philosopher's Stone, some of which destroy his shell from the inside. Unfortunately, Father reveals to Hohenheim how far he has evolved since they parted ways, emerging from his shell and eating it with the Philosopher's Stones it still contained, before restarting the fight. He defeats Hohenheim, restraining him with his body and later greets Izumi and the Elric brothers, who didn't recognize him at first. Soon after, Pride arrives with a blinded Colonel Mustang, giving Father his fifth and final human sacrifice.
Despite the alchemists' refusal to aid him, and Greed's attempt on his life, Father defeats his attackers and proceeds to finally activate the Nationwide Transmutation Circle around Amestris, using the restrained sacrifices' gates to access the Earth's gate while absorbing all of the Amestrians' souls. From there, in his full form, Father tears open the Gate of Truth with his bare hands; absorbing the higher power he calls "God". Once the transmutation process is completed, in a new youthful body, Father states to the alchemists how he "imprisoned God" within his body and possesses all the knowledge and power of "God". No longer needing sacrifices, Father cancels Alchemy once more and prepares to dispose of the five sacrifices, as well as Greed and May, at his whim by creating a miniature sun in the palm of his hand.
And he is reprised by Kent Williams in the English dub and by Akio Otsuka in the Japanese dub, as a tribute for Iemasa Kayumi.