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i'm gonna say its a separatist group of forerunners that decided to wait out the flood invasion rather than fight it, they wake up and cause havoc and have all sorts of classes within their ranks. It's possible that we'll perhaps fight forerunner AIs like 343 Guilty Spark or 032 Mendicant Bias. If not, then maybe the precursors. As for the secondary enemies, I personally don't think we've seen the last of the flood.

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