[Oddball]

OK OK
Here's my take on events.

We all saw Agent Smith infect that guy and then Agent Smith went from the Matrix into the real world (there is no matrix within a matrix that notion is just too simple and lame). Hence Agent Smith has some influence over humans (given certain conditions). This was most probably due to the tussle he and Neo had in The Matrix (film).

Therefore, Neo must have some kind of influence over machines. How far that influecnce extends...we don't know yet.

Get it? Smith has influence over humans. Neo has influence over machines.

Oh yeah and Neo is the first "Chosen One" to chose the door that he did (left or right I can't bloody remember)