Not a virus.... Just an old program that couldn't be off'd as said by the Oracle. To my understanding of the movie, Neo has always been "The One", it's just taken 6 times in reloading the Matrix in upgrades to be perfect. But with the twist that when Neo jumped inside of Agent Smith in the first movie, part of Neo was copied along causing Smith to be rebelious and understanding that he's not a program, but a programmer. Thus being able to copy himself at will. This is why Neo is getting stronger, cause he's now understanding that he can program himself to do much more inside of the Matrix. That brings us to the end of Reloaded and the question of did Neo stop the sentinals or was it an EMP? That will be answered in Revolutions if there is a Matrix w/in the Matrix.