The thing is everyone seems to think that there are 9 of The nine but the number nine can be used to represent alot of things. The nine could be one or they could be many. Also I think onimbus was a program or warmind because it's said that it analyzed the nine. And if I'm spelling it right. An onimbus is a cloud so it would make sense for this program to be analyzing space and our atmosphere.
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Well, the thing is, a survivor would look at a member of the Nine, and would think, well, these guys must be related to the nine crafts. Some one who watched the feeds would think that the nine were from those crafts, but wouldn't know what to call them. So he just called them the nine. Plus. That was were the Nine traded. They stay neutral. Ever wonder how the Winter Kell got a strange coin? He traded for it. There. Where Rasputin found the Darknesses forces gathering. I'm not saying they support the Darkness, I'm saying that they trade to everyone, no matter what their motives are.