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The time machine didn’t actually work, it just seemed like it work because of the same thing that created the paradox pokemon. The professor thought it worked and it created the impression that it did work. That’s why the only pokemon the professor was able to catch with it were more paradox pokemon despite the fact that the same paradox pokemon existed at least 200 years prior. There is some sort of missing link, possibly the “disk” thing mentioned in the book, that is turning people’s imagination into a reality.
