Heres the thing, Bane was "infected" by Agent smith. As you now know or assume that he is now set free, why? because he is obselete. As i understand it, there are 6 levels, or 6 recursions of the matrix. Every time the one, neo, goes to the father of the matrix, he goes into the right door and starts a new matrix, thus recurscion. However, i think agent smith is neo, or he was at least "the one" for a previous version of the matrix. Think about it, he keeps going through trying to stop neo. Stop neo from doing what you ask? Hes trying to stop neo from recursing again, and again, and again..........etc. This brings up the fact that the 'freed' minds are not really free but merely placed into another form of Matrix where they are lead to believe that they have control. Support you ask? When neo could feel the sentinals towards the end of the film, he stopped them from OUTSIDE the suposed matrix. This I concluded from the architect. telling neo that Zion had been destroyed 6 times before... That whole scene lead me to this.