When I first saw the ending of the Matrix Trilogy, I was somewhat disappointed at the ending. None of it made sense and it was a tragic way to end the trilogy. That is, until I read about a new theory that was backed up with plenty of evidence and logic. Here is my interpretation of the theory.
From the Animatrix, we saw that humans dropped nuclear bombs onto zero-one, the machine city. As we know from nuclear bomb tests, EMP (Electromagnetic pulse) is generated from the explosions. We also learn that this is the “only weapon” against the machines in the future. So how can such explosions fail against the machines? It doesn’t. In fact, the humans had actually won the war. Realizing their mistake in letting humans be some lazy, they changed their ways on a wide-scale because of the threat of machines (whether or not this is true is not relevant to my theory).
Because of the emotion-less machines, the war-won humans decided to make the machines learn emotions. They created a matrix for the machines where the world was what it would have been had the machines won. The matrix shown in the movies, then, was actually a matrix inside a matrix. The humans taught the machines emotions through each of the chosen ones. As explained by the architect, each one of the Ones developed a sense of attachment (emotion), in the case of Neo, love. Each one, then, were lead to the source so the machines could understand the new emotion.
The important part here is the idea of a matrix inside a matrix. This could also explain why Neo saw the gold colored lights inside the “real world” while blind. He actually saw the code of the original matrix much like the green code in his own matrix. The evidence for the gold colored matrix is very compelling: the sentinel that goes through Neo while he’s heading to zero-one (the code only, the machine itself hit the window), Neo’s ability to stop the sentinel with his hand, and his ability to see even while blind. All of this reflects his ability while he realized the illusion of the green matrix: he went inside Smith after “dying”, stopping the bullets with his hand, seeing the green code instead of what should be there.
Everything that people complained about that didn’t make sense seems to be answered with this theory. How Neo gained his powers, why the machines need to go through these cycles, etc. This is also further shown in the animatrix “Matriculated”. A machine goes through a process of learning from the humans; in the end, the machine sides with the humans.
