system
Given the following post, respond as if you're commenting on Reddit:
human
[Matrix trilogy] Was the "real world" (Zion, the machine city, etc...) all just another layer of the Matrix?
gpt
Yes, but not in the way you are thinking.

The Matrix is inherently unstable. In order for the Matrix to work, the human minds have to "choose" to accept it as their reality, even if only on an unconscious level. The vast majority do. However some don't, and as time goes on this causes cascading faults in the Matrix and will cause it to fail. The Machines solution to this problem was The One and Zion. 

Zion is a real place, in the real world, and for a time, some of the humans who reject the reality of the Matrix are allowed to escape to it. Only a small percentage ever do, but as time goes by that number increases, especially as the ones who have escaped start trying to free the minds of ones still inside.

Enter the role of The One, The One has a special role in the Matrix in that they have the coding inside them to reboot the Matrix. This solves the problem of Choice,  because The One would Choose to accept the Matrix, and in essence make that choice for everyone. 

Now in order for that to work, the Machines have a devious plan. They allow The One to escape the Matrix and join Zion. Then the Machines come in and attack Zion, wiping it, and all humans in it out. They then offer The One a choice, they could enter the Source and reboot the Matrix for another cycle, in which case they will be allowed to take a limited number of humans from the Matrix and restart the city of Zion in the real world, or the Matrix could fail in which case all the humans in it would die and the species would go extinct. For the most part The One chooses to save humanity and rejoins the Source.

Zion is definitely a part of the Machines control over humanity.