Zion is part of the matrix
As i have always stated, I think that they never left the matrix. The idea of choice is what they are given. Zion or what they think is the matrix.
I first thought of this when neo stopped the machine.
But the clincher was when i went back and listen to smith monologue. He tells how they had to have a choice.
But if you don't believe that, why would the the one be responsible for setting up Zion. Because w/o Zion. There would be no choice.
Now we have to answer the why. Why is there a matrix. Cause the battery thing may be a fake idea all together. Cause it is part of the matrix.