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Yeah, although I'm a little worried about you not introducing anything that new (new philosophies, a new point of view, etc.), I can get behind the rest of the idea. I want to point out a few issues:
mistakenly containing hundreds of personnel within their own facilities.
So nexus accidentally did this? Or did they consciously do it?
…they were blown off as being nothing more, or based on averages, and ultimately nothing to worry about. This negligence leads…
Most of what I don't like about these type of ideas is this trope where the competent scientists are suddenly incompetent, and I would prefer it to have more justification. However, a possible fix is to have the AI be very… charismatic? You don't have to humanise Nexus, but I'm sure it can learn how to lie and cover up all those tiny anomalies in its reports.
These are all the problems I have with this, I hope the critique helped. As it is, I don't really like the story enough to greenlight, but it is quite a solid one! Good luck in getting the requisite greenlights (and welcome back to the forums), War!