Originally posted by The Omega
Looking at the timeline, Zion (and probably other cities) were built underground in the last days of the war, and were strongholds of resistance/survival against the machines.

Now, since the Zion Database has survived some 500+ years, so we can see Second Renaissance, the machines obviously do not destroy Zion’s machinery. That would be like killing of a “sibling”, and would make it hard for Zion to serve it’s control purpose.

Every woman., man and child ARE killed. The place is probably in ruins, but it’s not beyond repair. The previous One with his 23 people arrive to this ruined city and rebuild it.
Not from scratch.

Thats kinda what I was saying. Excluding my theory that the original zion really was the last stronghold of humanity after the war.