For example, humans may incorporate the machines into themselves. We become partially Cyborgs.
I would call that "the machines took over". If the thing that you incorporate is smarter than your human brain is, then that thing is "the boss" and you are just its biological support. If you incorporate an exo-skeleton, then that exo-skeleton augments your abilities as a human. If you incorporate an electronic brain that tells your body how to act, then YOU are the bio-skeleton of that electronic brain, no ?
The command is where the intelligence resides. The "thing that is alive" is the deciding entity. My only argument is that at a certain point, machines will outsmart people (biological people). Simply because machines can be improved much easier than humans (biological brains), so the slope of the machine intelligence curve is steeper than the one of human brains.
Once machines are smarter, they will be in control, simply because they are the smartest entity. It won't be a human brain that is in control. It will be a machine, even if "you" transplanted your brain and got a piece of silicon in your head. Then that piece of silicon is "the machine" and not "the human". If it controls a human body, that doesn't mean it is a human.
I don't know the relationship between humans and machines. Maybe we will be "machine's best friend". Maybe they will care for us, like we care for dogs and cats.