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I was going to ask why the machines do not kill everyone who is woken from the Matrix, below we are shown a scene where Neo is woken from the Matrix,

They potentially have the power to keep things in check purely by killing anyone who wakes from the Matrix. I am not talking about being flushed down a sewer to drown and possibly be saved by a passing ship, I mean having the machine lop that persons head off right there and then. And since they have destroyed Zion several times and just left several people alive to reset the cycle all over again, no-one would be left in Zion if the machines so desired.

I understand that the computers need an anomaly to reset the matrix and restore balance. But why the need to wake "The One" from the Matrix. Couldn't the machines have achieved the same result within the Matrix by simply showing Neo what he could do indirectly with a "Program" design to teach "The One" how to do all the cool stuff he does and to have other "Programs" to rebel against the machines like Morpheous and the others do. This would serve the same purpose of getting the one to make a choice when he is the meet the Architect without the need to go in and out of the Matrix.

This way they would have full control and be able reset the cycle with minimal effort.

Assuming the need to have the anomaly fix the issue within, So why even the need to have "The One" woken from the Matrix?

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There's a few things going on here that would prevent the world of Zion being recreated in a virtual layer of the Matrix;

The "mind-splinter".

Morpheus describes the feeling of being inside the Matrix as one that is instantly recognisable to those who're aware of what they're looking for

It's that feeling you have had all your life. That feeling that something was wrong with the world. You don't know what it is but it's there, like a splinter in your mind, driving you mad,

If there was a secondary layer of the Matrix, those who're unsatisfied inside the Matrix would be unsatisfied in that second layer as well. The Architect makes it clear that he's simply incapable of building a realistic world despite having plugged away at the problem for the best part of a millennium.

The Choice.

One of the main reasons that Neo is shown to the Keymaker by the Oracle is to allow him to make The Choice, a specific promise to accept the Matrix in return for the continued survival of the human race. Echoing the 'Instrument of Surrender' seen at the end of The Second Renaissance, Part 2, it would appear that the machines are simply unwilling to continue running the Matrix if the humans aren't willing to be in it.

If you trick the people's proxy (Neo) into making a false choice, that would invalidate their moral superiority, hence why the Architect tells Neo about Trinity's presence in the Matrix and her impending death. A false choice is no choice and no choice means the end of the Matrix.

Neo - You won't let it happen, you can't. You need human beings to survive.

The Architect - There are levels of survival we are prepared to accept. However, the relevant issue is whether or not you are ready to accept the responsibility for the death of every human being in this world.

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