[Crash]

well, it had to be part of a simulation that the machines made. in the regular matrix, the agents have to "conform to the normal laws of physics" so the machines stuck neo in his little matrix adaptation (same kinda adaptation as the train station, still the matrix, but different rules {remember trainman saying "downhere, I make the rules, downhere I am God"})

so see, they can do a matrix inside a matrix... thus i stick to my original theory

Here is my complaint though, if the smiths have to conform to the normal laws of physics, and like in the first one, if you "kill" an agent, they revert back to who they took over. (saying they can die just as easily as a normal human) how did smith body slam neo from 2000 feet up into the concrete ground and not break every bone in his host's body, and die?