My question is how is Naobi still in Revolutions when she was killed in Reloaded....
Honkeytonk: I don't think your first theory quite works. Since it looks like there is a major battle between Agent Smith and Neo in Revolutions I don't see how they could be on the same side. Also he did almost try to kill Neo in Reloaded. But maybe his flaw in the matrix allowed Neo to break the infinite loop of The One created by the Architect.
