The Matrix Resurrections picks up 60 years after the original film trilogy. Free people have left Zion for the hidden IO in the movie. The question, of course, is what happened to Zion.
The new enclave, IO, is grander, more spacious, and more prosperous than besieged Zion. The new film expands on the franchise’s mythology and explains Zion’s fate.
The Matrix Resurrections and IO
In The Matrix Resurrections it is not Zion where the surviving people live, but therefore the city of IO. A completely new city populated by completely different parties.
Through General Niobe we learn in The Matrix Resurrections that Zion was destroyed in a civil war among the machines. For a long time they had really kept to the agreement with Neo and Deus Ex Machina. People were allowed to go out of the Matrix to Zion.
But the Machine World suffered from the massive energy crisis as a result of the many people leaving. That led to a kind of war for resources between different machine factions and that war spread to Zion. Humanity had to flee and build a new safe home.
IO was eventually built by people and machines who had fled. This naturally makes things more hopeful and optimistic.