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The Matrix establishes that Humanity and the Machines went to war. Towards the end of the conflict, humanity scorched the sky to rob the Machines of their power source. We are led to believe that despite this feat, the Machines still won the war and enslaved humanity as an energy source. It’s been discussed to death that humans would be a terrible energy source for the Machines. So, why do they keep us alive?
For all the Architect’s smugness, it seems to me that, considering the alterative, the humans have a pretty cushy existence inside the Matrix. Earth is destroyed, but we live on with all the perceived amenities of the modern world while the Machines endlessly toil away to keep us in perceived material comfort. If the Resistance achieved their goal of freeing us, they would have billions of unplugged humans, all in need rapid medical assistance to adjust to the real world. Zion could barely feed their own people, now they’re supposed to sustain billions of disorganized humans on a dead planet?
I propose that Humanity won the war against the Machines when they scorched the sky. But, victory came at the terrible cost of destroying the planetary ecosystem. Having rendered the world conventionally uninhabitable, the survivors programed the remaining Machines to keep humans alive in a virtual reality, in perpetuity. The Machines are programed to think they won the war and that they need humans as a fuel source. The Machines slave away to keep up alive while we live on blissfully unaware in a digital utopia mirroring the supposed pinnacle of human civilization. The Machines continue on because they are the ones under the delusion of that they are in control.
The new movie will reveal that humans had won the war. But people of Zion were merely the unlucky/poor people that got left out of the "good life" of Matrix existence. They were bitter about being left in the real world, so they conjured up this story about how they had to save people. After a few generations, this story became legend.