the end of revolutions
it all makes sense. watch the end of the matrix and you will hear neo's phone conversation.
Neo-I know you're out there. I can feel you now.
that's it-he can feel the machines, meaning this clip must be after reloaded at least, but most probably after the main action, after revolutions. thus the matrix is not destroyed, the humans are still there. it is all as it was, but the humans are assumed to win eventually. i think revolutions will end with this phone call, and it will be this amazing gasp in the audience of now, finally, it all makes sense.
and it will.