At one point in the game Cortona says, according to what they showed at E3 "Chief...their coming back, and this time, theres ALOT more of them!" and they confirmed we met them in one of the games, I'm inclined the think thats it's the flood becuse there an extragalactic species, who knows how many other galaxies they have tried to destroy and sucseeded.
And Mythionion, Galactic civ. 2?
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