The Real Reason Zion Is Allowed To Exist In The Matrix Trilogy
In The Matrix series, Zion is the last bastion of human civilization outside of the Matrix. Humans who escape the programming come to Zion to find a new life and join the resistance against the machines that rule the Earth and use the rest of humanity as batteries. When we first see Zion in The Matrix Reloaded, we learn that the city is incredibly destitute despite its advanced technology. There aren't many humans to go around, and everyone is struggling to get by as the war takes a continual toll.
This raises a huge question. If the humans are so weak and the machines control most of the resources on the planet, how does Zion still exist? Sure, part of the primary conflict in The Matrix Reloaded is that there's an overwhelming army of machines just a few days from drilling their way to Zion, but the war has been going on for generations. Theoretically, the machines didn't have to wait this long to wipe out the human resistance. So why have they let Zion survive all this time?
Zion exists because the machines need it to survive
To the machines, Zion is a necessary evil. As the Architect (the program responsible for designing the Matrix) explains in The Matrix Reloaded, all of the series' events up until the present storyline have been orchestrated. This includes the prophecy of the One. In reality, Zion could have been destroyed much sooner.
However, the machines actually need Zion to manipulate the One. As it turns out, humans always have the subconscious decision to accept or reject the Matrix's false universe. In large numbers, this would lead to the Matrix crashing. However, a single human integrated with a program can act as a surrogate for humanity's individual choices. Should Neo return to the Source and "accept" the Matrix, Zion won't be fully destroyed, and he can pick a small group of survivors to rebuild.
It turns out that this entire process has already happened five times, marking five different iterations of the Matrix. If Neo chooses not to continue this cycle, however, Zion will be annihilated, and humanity's last hope for survival will be gone forever. At the same time, this would also mean that the Matrix crashes, and the machines would eventually die out without a consistent source of energy. It's a no-win situation for the humans and a risky but rewarding exchange for the machines — leading to a satisfying and thought-provoking ending to the trilogy.