Ok here we go….
Ok, my theory is that they’re all still in the matrix and the creator guy (who’s really a program within the matrix) was actually telling the truth. Neo is a virus (who’dathunk) and the computers running the matrix came up with a means of keeping him occupied by creating the messiah theory. The people in Zion are still in the matrix, however, they’re running programs that put them there, including those that think they’ve been ‘saved’. All to keep Neo, that little bug, busy. Now, the reason I think this is due to his last interaction with the sentinals, and the fact that ‘Agent Smith’ was able to infect that other guy’s body (the one who helped wipe out Zion with the EBM blast).
However, I think Neo realized that he is still in the matrix. Granted, I don’t think he quite realized it when he ran out to save Trinity, but he did when he disabled the sentinals. Which, leads to the fact he’s now a rogue program who’s now committed to finding a means of destroying the matrix without killing everyone who are acting as batteries (which he was told would happen by the creator’s program). I’m not sure what to think about this other guy yet, but I’m quite sure he’s going to be the antagonist in the next episode and is probably a program that will end up acting as the key to saving all the batteries.
Ok, that is all for now.