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Magnemite is an alien.
It's based off the fuel core Bob Lazar claimed fueled UFO's in the 80's.
This is supported by Magnemite's anti gravity dex entries.
Essentially Magnemite is a sentient alien probe/ fuel core, that eventually evolves into a full on UFO.
The magnets and screws are a little more difficult to explain, but they could either be coincidence that they resemble magnets & screw but arent actually magnets or screws. Or the aliens/ ufos they originate from are actually future time traveling earthings.
