The Matrix is really just about humans being enslaved by machines and wanting free.

The Matrix is another universe too, in the sense given in my plot summary.

I hate stories like the Matrix though. Good stuff in it but humans are always assuming that they are the ultimate good and that the value of their lives overwrites anything else. That usually results in machine racism like what happens in the Matrix. If we survive long enough and continue on our same trend of thought, this will be a problem in the future.
If you watch the Animatrix, you'll see that the humans actually did some real bad shit to the machines.

Retardation excused.

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