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Part of it is speculation, but I do remember a fair bit of stuff from the previous games as well as a bit from the new one where Hideo said that the factions came together for the benefit of everyone when the cabal attacked.
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And in the big scheme of things the 3 idiots don't realize they are stronger working together... I mean c'mon mesh their ideals together and humanity would be a whole lot stronger. There's nothing wrong with seeding across the galaxy, meeting new races and helping them out, facing new threats etc... this whole shtick of pick one or the other is so simple minded...