The Godfather movie series is an alternate universe, not just fictionalized romanticized Mafia fan fiction. At the end of the first movie (notionally around 1959 or 1960) Michael Corleone has all the other New York bosses hit. So unlike in the real world 1960s, there is only one Mafia family in NYC instead of the real world five. The Godfather III becomes more plausible with this interpretation.
Childhoods End (book and movie). The Overmind is just some morally neutral mind eating entity, and the Overlords were getting rid of potential competition.
The Matrix. Zion (a.k.a "the real world") is just another part of the Matrix, as a safety valve for the main Matrix. For folks who need to be action heroes. Morpheus is an "agent". And the bit about using people in Matrix as batteries is pretty implausible, so that's just another cover story. It's to get everyone out of the way without killing them, because Asimov's Three Laws still apply, even in an hideous dystopia.