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I think these are the last major questions without answers. With the limited information we have and using the least amount of headcanon to fill gaps I would wager my guess on the time machine being pointed at Area Zero 200 years ago. It takes the paradox pokemon from that time period, which is where the AI winds up when they enter the machine. An important plot point they never cover in the DLC is the time machine being a one way trip for humans.
I guess the other unanswered question is how the book gets back into the professor's possession. They learn the name of the Raidon from you as well as the idea of building the AI, so it's possible they just get the book back from them.
