When higher vertebrates developed cerebrums, those didn't replace the evoluntionarily-older cerebellum or midbrain. We humans still have those. From the perspective of a lizard, a human looks like a lizard with an awesome AI-like cerebrum strapped to it.
Importantly, the cerebrum does not have an independent self-preservation drive.
Frankly, I think "AIs with their own self-preservation drive and plans for the future" is implausible, although it is likely to be put forward as a deceptive explanation of what's going on by the first few humans who figure out how to strap on another layer of cerebrum. It's the easiest way to keep the rest of us from becoming resentful.
Come home, all you commodores, come home...