Creating the Homunculus was the final stage of the Human Isolation Project by the Innovation Empire. They created the perfect human by excluded human's biological mating and using informational knowledge to distinguish between and mate a truebreed. This new being has DNA that's totally different from that of a human.
Ten Homunculi were created to break the bounds of human DNA. They have a long lifespan and an outstanding body condition. They can even survive and function in the vacuum of space.
An incomplete 11th Homunculi, Eve, was created due to the appearance of the Beasts. It was the same battle organism as the N.R.A. which they hated so much. It was later sealed away at the 4th Ground Zero, where the Homunculus ruin exists. (AE2 - Ch7)
Appears in AE2 (Part 6) Chapter 82.