Plot twist: Machines didn't take over, but some other entity did (aliens, other humans or maybe even some other weird and abstract concept of something) and the

Plot twist: Machines didn't take over, but some other entity did (aliens, other humans or maybe even some other weird and abstract concept of something) and the Matrix is indeed just some decoy to hide all the other meta layers, which in the end result in the truth that basically everything is a simulation, including the concept of said entity taking over something to run this simulation in the first place ... or they pull off the super disappointing "everything was just a dream" meme. Sounds like fun to watch in any case!