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The thing that I'm hung up on is the inconsistencies with the AI. Their initial communication to bring you to Area Zero they lie to the MC. While you're deactivating the locks (that are keeping the AI inside of the lab) they tell you specifically that the time machine is a one way trip "for a being such as a human".
How do they know that? Who was sent through the machine? Were they sent previously or did the professor not actually die and the AI lied to you again?