@ISingTheBodyElectric Yeah that's a good theory, the outside world looks like it has crumbled, so it'd be pretty ironic if he killed the remaining humans to be in control of a wasteland, and the only human left is Alice, which he can't control.
With this reveal, I wouldn't be surprised if Alice is an existence similar to the Snake and is just bored after having already destroyed the outside world. It would explain why the book smelled like her brother