If the first One was as Morpheus describes in the film - could make the Matrix over as he saw fit - and led the first of us out
The One would be able to self actualise
We saw what happened when Neo woke up in the pod, gets flushed, and rescued by the ship
So how did the One get out and get the others out
Would they just wake up in the pods, get flushed, and by floating around in the water, unable to swim because they had atrophied muscles
Zion would need to already exist in some form, and so would at least one ship for them to rescue the woken flushed bodies before they drowned
This makes sense because there would be some humans who were never captured - think about the Terminator films - the first film where we see Reece go to the camp
If the humans were not resisting military style, which would be pointless at this stage now the world is conquered, the machines would not be aware of them or be looking for them
This would allow them to escape, get underground, and build Zion
