JediHDM
Jedi of the Matrix
allow me to explain it in a different way, if you will...
Smith was of the Machine's, we know and acknowledge this. The Architect was there to balance the equation. As long as Smith is there, and Neo is there, the equation is balanced. However, the Oracle, knowing that the only way the humans and machines can live together, is if the balance is unbalanced, rather, if penance is paid for all the humans did to the machines. This is Neo. Neo is a sacrificial lamb, so to speak, for all that the humans did to the machines. The humans erred, and Neo must make up for that. So, he makes a promise. If he stops, or allows Smith to be stopped, then the Machines would allow the humans to live. The Oracle understood that burden placed on Neo, and tried to help him as much as she could, without telling him what he has to do. This is choice, and only a choice that Neo himself can make. Thus, Neo goes to fight Smith, 1 vs 0, beginning and end. Neo didn't really understand the choice he had to make, really, didn't understand his purpose, until he was beaten, laying there in the mud, and Smith made his mistake. In his (humanlike) pride, he remembered what he had seen when he took over the Oracle. He remembered that he wins. So he says it. But it isn't him saying it, but rather the Oracle speaking through him, when he says "everything that has a beginning has an end, Neo". In that instant, Neo understood everything, understood his purpose, the Oracles purpose, Smiths purpose. he understood that, the equation must be unbalanced if it is ever to be over. So he allows it to happen. He allows the 1 to be overtaken by the 0, creating an unbalance. Smith is happy, because he thinks it is over. And he is right. When the equation is unbalanced, it must be balanced. thus, the source sends out the anti-virus, or whatever you want to call it. However, it effectively removes Smith from the system. Neo glowed because it showed the enormous power flowing through him, the machine code that was being transferred to the Smith-source, from the source, through one of the smith-virus' own clones. And now Neo glows, a testament to the fact that Neo is, in fact, alive, perhaps not in body, but his mind is very much alive, and it is now a god-man, or a machine-man, a complete yet mixed entity, comprised of Man and Machine. He is truly the lotus blossom.
wow...i kinda rambled on there...hope that helps.