Melissa left me a voice mail asking about the ending part of the movie, with the fight scene between Smith and Neo.
Well, when Smith takes him over, Neo is considered dead. He actually is dead in the real world, for the oracle states that Smith is basically the exact opposite of Neo. It would be like Ying and Yang, night and day, good and evil. If you remove the one, the other goes as well. Neo figured this out and allowed Smith to overtake him, thus "killing" Neo, and thus "killing" Smith, and all of his copies. Everyone else in the Matrix, including the programs, goes back to normal.
At least, this is how *I* saw the end of the movie.