Some of this is from the Torah, some from rabbinical commentary, some from oral tradition, and probably a number of inaccuracies caused by my fuzzy memory on the subject (PLEASE feel free to set me straight if you know this better than me). Please bear in mind that this is not necessarily my take on the whole thing, just the story as I recall it. Here’s the gist:
Following the Morningstar’s failed coup in heaven, there was quite a bit of aftermath that lasted well into the book of genesis (the fate of the neutrals, etc). It almost seems like the power structure was not quite settled into the classic good vs. evil dichotomy that we associate with judeo-christian perspectives. During this period of vagueness, there were a number of disobediences on the part of the angels, particularly in the lower choirs. One such incident involved a number of Grigori (the watchers) who became infatuated with mortal life. They decided they wanted to go down to earth and have wives and children, AND retain their divine status. Exiting heaven and becoming mortal was not unheard of, but these grigori cheated a bit on the protocol. They impregnated the women they were set to watch, and fled from heaven afterword, fearing God’s wrath at their transgression. They settled down with their wives and raised their children, who, by virtue of their mixed parentage, had incredible physical (and some say majickal) power. At this point that first sin in existence reared its head again: pride. These half-angels were far more powerful than their human counterparts, and began to run amok, killing as they saw fit, viewing humans as inferior and thus not worthy of consideration. You see, they inherited something else from the angels: a lack of conscience. Angels did not really possess a conscience as we understand it, rather a consciousness shaped around a function. With this great power and no conscience to temper it, the angel-born made life quite difficult for their human kin. Humans began to worship the angel-born as gods, willingly offering their own born as sacrifice. The grigori were proud of their children, seeing their power, and declared that they had put on the earth a race greater than that which god had created. They believed they had, with the power of their loins, surpassed God.
It seems that God was OK with letting the angels slip out and taste the domestic life, but when their children began eating humans (as we eat species of less power than us) and the grigori chirped their pride, God intervened. He sent the Metatron and a seraphim to speak to the grigori three times, each time asking the grigori to reign their children in, that they may live at peace with humanity. Each time the grigori scoffed.
The first time metatron came accompanied by Michael, who asked that the grigori do what is just and let balance and justice be restored to the earth. The grigori replied that it was only just that their descendants eat men, as man ate lamb. Why should their children act any differently?
The second time metatron came accompanied by Raphael, who asked that the grigori do what is intelligent and reasonable, pointing out that a cooperation was better for both sides. The gigori said that it was only reasonable that their children rule man as they wished.
Since the intellect of man was insufficient to save them from the angel-born, of what value could it be?
The third time metatron came accompanied by Gabriel, who asked that the grigori show mercy to humanity and withdraw their children to a separate place. The grigori laughed and said that it was a mercy to man to strike them from the face of the earth, rather than have them live as a failure. They had been intended to steward the earth by God’s command, and they had failed. How merciful is it to leave them living, spawning generation after generation that would fail in their holy task, sending generation after generation to knock at the Morningstar’s door?
The metatron came to the grigori a fourth time, and this time the seraph that came along asked no questions. The angel that came was named Uriel (uziel), and it spoke thus “You have been asked three times to control your children. You have refused to be just, to listen to reason, or to be merciful. He who is I AM has sent me to deliver a message. Because you will not be just, reasonable, or merciful, the choice has been taken from you. God has seen his children slaughtered, and will be just. God has seen his children treated as beasts, and will act according to reason. God has heard his children’s prayers, and will be merciful. Because you have refused to intervene, your children and those that follow them will be destroyed, and what remains will be scattered. They will be Nephilim, outcast and landless. Know that you have spoken with the Angel of Justice, Thought, and Mercy. Now you speak to the Angel of Death. I will bring the only justice, thought, and mercy I can.”
At this the grigori begged that their children be spared. They wept bitter tears, and seeing this Uriel said “You cared nothing for the tears that have been shed, so it will be tears that bring what I have said to pass”.
At this time, there was a righteous man named Noah….
you know the rest.
That’s it, a few literary indulgences (dialogue. I’m a sucker for dialogue) aside. Some of the Nephilim survived by sealing the mouth of a cave and waiting till the waters abated.
Again, this is not necessarily a representation of my take on the whole thing. I’m just presenting the traditional story as best as I can recall.