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As explained in M1, the machines need humans for power

but they only use them for power in the fields of crops

why does the architect/ the machines want the one to rebuild zion so they can destroy it again why bother having a matrix at all, why cant the humans just be grown at the crop fields.

Prehaps i need to see both films again, am i missing something

Take a read of this:

http://www.killermovies.com/forums/f42/t9814.html

Brief explanation of things that have happened so far...

so basically the human brain has to be active for the machines to use their power