GRAND ANTI-MULTI-MATRIX (GAMM) THEORY
A. Path A
Let's take (A). Assuming 100% of humanity was found/enslaved, then Matrix Software Version 1.0 (MSV1) and Zion Software Version 1.0 (ZSV1, another program) were created for the physical Matrix Hardware. Obviously, MSV1 failed miserably and numerous human "crops were lost," lost either by suicide or fighting Agents. Those who fought Agents must have been unplugged by those from ZSV1. Thus, the first "One" was born, unplugged, eventually reached the Architect, and chose the "Source" door to unplug 23 people from MSV1 so they could repopulate the "destroyed" ZSV1 into ZSV2, and to keep the remaining humanity in MSV1 so it could be reloaded/upgraded into MSV2. So far so good?
Question A1. Why would the machines CREATE ZSV1 in the first place? If ZSV1 never existed, nobody would be around to unplug anybody in MSV1, nobody would know about Agents, nobody would die fighting them, and the "One" wouldn't emerge at all. This doesn't happen. SOLUTION: There was no ZSV1 in the first place.
Question A2. Assuming ZSV1 was created, why would the Agents want to KILL anyone unplugged in MSV1? ("Everyone who has stood their ground, has died," says Morpheus.) Knowing that killing would deactivate a human power source, the Agents wouldn't kill, but would let unplugged humans escape into ZSV1, and let the Sentinels "destroy" ZSV1 anyway. But Agents do kill. SOLUTION: The Agents don't want unplugged humans to escape, since there is no ZSV1 to backup MSV1.
Question A3. Assuming ZSV1 was created, AND assuming Agents killed a small percentage to give the larger percentage the illusion of escape into ZSV1, why design ZSV1 to be an underground city with enemy Sentinels? (Here's my "aliens" angle again.) Wouldn't it be more logical to design a city-world that gave no clue of Sentinels or machines at all? Why not lizard-aliens like "V" or ape-soldiers like "Planet of the Apes" to throw off the scent? SOLUTION: There is no ZSV1, since Zion is real, and the Sentinels are real.
Question A4. Assuming all the previous assumptions, AND assuming the machines didn't care about revealing their true selves in ZSV1-to-ZSV6, why go through the "play-acting" process of "destroying" and "repopulating" ZSV6? Couldn't ZSV6 be "reloaded" just like MSV6? Why pluck 23 people from MSV6 to "repopulate" the supposedly "destroyed" ZSV6? SOLUTION: Each Zion was real (perhaps in different locations), each destruction was real, and each repopulation was real.
Question A5. Assuming all the previous assumptions, AND if Neo chose to "destroy" MSV6 (by saving Trinity) and its billions of human batteries, why would the machines continue to "destroy" the remaining quarter-million batteries in ZSV6? The machines would prefer to keep ZSV6 intact. So why don't the machines "transpose" the intact ZSV6 with a much-smaller MSV7, and then "reload" a smaller Zion ZSV7 with a few people from ZSV6? This would all occur in the same physical Matrix Hardware. The Architect has no reason to lie to Neo, yet again, why does he refer to ZSV6's "destruction" not "reload"? After all, all of Neo's friends would still be alive in ZSV7. SOLUTION: MSV6 is the only human power source, ZSV6 never existed, Zion is real, and its destruction will also be real.
B. Path B
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