The Real Villian
I think Ilias is the good guy in this story, as we see throughout, the monsters always try to take advantage of Luka, even the ones claiming they want coexistence, they all rape him, I think Ilias even points this out at one point. The monsters are selfish and only care about what they want, they don't care about what happens to others and do as they please to whoever they please. The only reason they decide to coexsist is because Luka defeated everyone in high power, forcing them all to submit. Ilias's idea to genocide was a good idea, there was no hope for the monsters.
Timeline Theory
Long before the events of the game, and long before the creation of Ilias and Alipheese the first, humanity had reached a milestone in their advancement in technology, the ability to create living beings. These beings created by humans are Ilias and Alipheese the first, humanity did their best to teach Ilias and Alipheese all they could about morals and emotion, and the difference between right and wrong. Their gained supernatrual powers as a result of this new technology that created them, and rivarly soon grew between the two, always trying to out do eachother, their rivarly soon turned physical and fights broke out between them. As their fighting continued, humanity suffered greatly from the destruction they caused, so they attempted to…