Technologically advanced aliens wouldn't sneak around working with governments etc. They'd just bull right in and take over, same as the technologically-advanced Europeans did with the rest of the world.

What everyone forgets is that both ofr the aliens and human governments, such shenanigans would be incredibly expemsive, with little or nothing to show for it. Governments are not, on the whole, keen on the long view - they want whatever it is done in time for the next election so that they can get the votes in off the back of it.. Likewise, dictators or other non-democratic governments want and need results to keep people quiet and compliant.

These things have been going on since apparently, the 1940s at least. Seven decades with n visible outcome or profit. All our technological advances have a provable human 'pedigree', so we aren't getting them from elsewhere. Seventy years pumping in money withotu visible gain? No government, human or alien, would put up with that!

No, whatever is going on in underground bases in remote, thinly-populated areas, it's all entirely terrestrial! Weird, inhumane, potentially illegal possibly, certainly unethical and probably lethal, but completely human!