Here is 1 theory *SPOILER ALERT*

Rating: 9/10 (8 November 2003)

*SPOILERS AND BAD SPELLING WITHIN*

Ok here is a thought. Agent Smith was able to steal a body and get into the real world via the host. I think that Agent Smith had become a virus which was why he was duplicating himself into other programs and people. So what if when Neo was born he was in reality an anti-Viris Program that had been installed into a new born. He grew up met Morphius was released from the Matrix (Still a program in a human body) then at the end of Revolutions Neo absorbed the Viris (Smith) and was able to repair the corrupted files.
To discuss further (or check to see if i've been taking my medication) E-mail me at scandalsheets@hotmail.com