Oh my goodness I've just learned a thing about The Matrix that causes it to make a lot more sense: In the original script the humans were used as neural network compute clusters by the Machines and as a crucial component of The Matrix itself.

Which is why humans who were aware of the simulation could control aspects of The Matrix - their minds were part of its foundation.

Unfortunately the test audiences had trouble understanding this concept so the studio changed the human role to "batteries".


Hyperion novel spoilers 

Weird coincidence. In Dan Simmons' Hyperion, the Technocore uses the human brain to power their computing network. Except instead of keeping humans in pods, they use telecasters to teleport humans, steal computing time from them, and later teleport them to their destination.

Further spoiler: And later, they use cruciforms.

Hyperion novel spoilers 



I was thinking of precisely the same thing!

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