Vaskez, let us assume the "real world" is real. Reading a bunch of the above stuff, from philosophy about a perfect system needing choice and imperfection, to common sense practicalities, "The One" program was created to reload the Matrix. Well, "The One" program can't exist unless "The One" can escape the Matrix, learn the truth of existence, and find the Architect.
In order for "The One" to exist, then, rogue humans must exist to propogate and fullfill the Prophecy. Well, the computer creates rogue humans by unplugging especially talented folks and letting/helping them find/build Zion. If you are thinking "what about Tank" or other "Naturals," well over generations they are born. Neo and Trinity would have a "natural" as a child, for instance. Anywho, over time, the community grows, the prophecy grows, and The One is "born" -- a human with special talents and perhaps a special program or two for high-speed operation within The Matrix.
Remember, guys, Neo IS part machine. He can't forget what he "knows" and that means, I presume, his statement "I know Kung Fu" means he knows it in the real world too (even though gravity applies
).
Anyway, The One finds the architect, realizes that humans will die off completely if the machines die off, and chooses the "reload" door. Then, the machines descend on Zion, kill people, limit the numbers, kill the historical memory, and go pull a few new folks from the Matrix to start it all over again.
Whew -- fingers need a break. Maybe more tomorrow.