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I was just watching a video the other day where the theory is put forward that Zion with the inhabitants is a backup recovery system of the matrix. That is, the main AI system-the architect, agents, can only control the software part without new errors, the part that exists unchanged since the design of the matrix. But there is a possibility of an internal error that destroys the system (Agent Smith) This is a side effect of AI's free will. After all, Smith didn't become a virus after Neo destroyed him for the first time. He had already pulled out his earpiece (going against the system) and talked about how much he hated people (the main power source of the system). That is, the danger to the functioning of the matrix is not in the free will of people (this is an illusion), but in the newly manifested free will of some part of the AI. Previous versions of the matrix were destroyed not by Neo or humans (the architect doesn't say this), but by Smith or a similar virus that previous versions of Neo couldn't handle. To do this, the AI core (architect), when designing the next version of the matrix, creates a backup recovery system that has freedom from the main part, but in fact initially depends on the creator of the system. These are the Chosen One, the people of Zion, and software non-standard tools: Pythia, Seraph, Merovingen and company.
This theory is confirmed at the end of the film. SPOILER ALERT. Neo agreed with the architect to continue the work of the matrix and destroyed the main error of the matrix — Smith, but the matrix itself was never destroyed (and should not have been according to the original plan). In other words, the tools used to restore integrity in a critical situation only worked.
Neo's connection to the system is traced in the moments when he stops robots outside the matrix and sees the world around him without the help of his eyes. In other words, it has tools not only inside the simulation program, but also controls outside of it. These tools, from a materialistic perspective in his mind, could not appear out of nowhere, except to be initially integrated by the AI core.
This is one of the versions. Another version is that the world of Zion, along with the entire engine, is another higher level of matrix simulation.
The third version — the last Neo was still completely free, not only in the matrix, but also outside of it. That is, he brought consciousness out of the causal relationships of the material world. And the decision to save the matrix was made out of compassion for the people who would have died if it was destroyed.