An Interesting Theory.
Here it is:
Think back to the first Matrix. Remember the date at the beginning, when Trinity is contacting Cypher? It is 2-19-98. Now, think about the date they showed at the end of the movie, before Neo flew away. It is 9-18-99. That is exactly 1 year and 7 months apart. Now remember: Matrix Reloaded only takes place 6 months after The Matrix, the events of that movie and Revolutions consists of a matter of about 9 or 10 days. So, if you put all these things together....then this means that the scene where Neo flies away after talking on the phone, happens after the events of Revolutions. Which means he survived as some sort of program. And this cannot be coincidence, because the Wachowski brothers planned all the movies in one big story. Anyone have any thoughts?
Please don't bite my head off if this has already been talked about: because I tried to search for a thread on it, and I couldn't find one.