When Deus Ex puts Neo into the Matrix he meets Smith on the raining city street
The whole place is different
When the humans are watching the feed they ask if something is wrong - no, this is how it looks, it has been completely changed remade
Smith says to Neo "Do you like what I've done with the place?" - he has remade it how he saw fit
Everyone standing there is Smith - there are no more individuals - everyone is Smith
The One