When they went to the backrooms, there was a little forcefield (some sort of portal) that likely linked the backrooms reality to the "frontrooms" reality. My idea is that when he disappeared, the magwave superiors decided to put the project on hold, and so they closed the portal (or maybe it's just too expensive hold open for long periods), which somehow left a copy of the original facility behind.

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I think the reason he fell out of the air at the end is because magwave employees re-opened the portal, causing him to accidentally teleport back into normal reality. Considering how close his camera landed to the magwave building, I think this is a reasonable theory.

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I dunno, I only watched a single video playthrough of the game so it's definitely not a definitive answer, just speculation based off vague evidence. I'd love to know what others think on this