Actually, if your hypothesis is correct, and it's all within the matrix, why isn't it just another reset of zion? Why don't they just clone Neo and Trinity again, like before, and restart the matrix?
For the same reason they let the people "escape" from the first layer.
So that they struggle in the second one and provide energy for the machines.
It doesn't cost the machines any extra energy. It's all just one big simulation with multiple layers.
I don't think you're accurate with that.
Doesn't matter though, because they still went full retard even if you were.
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