In the control ending for Mass Effect 3 it has been made out to be a sorta entity type ending. As we see Shepard become some sorta new life form that takes the Catalyst place as the head master of the Reapers. Depending on your morals changes what will happen as you either become the galaxy police or watch dogs if your Paragon or middle ground. In the Renegade version the Reapers take control and Shepard becomes a dictator that rules with an iron fist that will do whatever it takes to get the job done just like a Renegade Shepard. The Reapers just become changed though all at once so it might be that they are shackled AI that represent themselves as gods.