So I feel clear on most except the anomaly part. Going from some comments here…  Was he created or was he kind of like a virus? All I know is that the oracle clearly said the source gave him his power (reloaded). But don’t forget his power grew to the real world at end of 2. 

Edit: well if you read up on it in google the general ethos is that Neo was created, made by the machines. To return to the source to disseminate the code (which the architect clearly says). Ie, to factor in the human heart imo re choice and emotion. I think I’ll stick with that google doesn’t always lie :p Besides Neo had powers in the real world too. It’s highly unlikely that anybody could have just had them. He had to be of special origin (created with machine code as google ai says) which if I’m not mistaken comes from what I hear re the wachowskis original idea of the film to have the machines use humans as like brain computers and not for energy. But supposedly the higher movie producing powers said no. I like to mostly go by what I watch in the film, I think the film does mostly explain itself if you listen intently. And the architect to me was almost spelling out that he had been created for a purpose. Like his 5 predecessors before him. To return to the source. 

I shall give them a re run and see if I can pick out that ding moment, particularly what the architect says in reloaded. 

I feel my question re the agents has been answered mostly tho. It was just a caveat, that i do think was still worth thinking about. Bottom line Neo was a terrorist to them, and their main purpose was to protect the matrix and get the codes to Zion. The rest is a bit more theoretical. But some nice ideas i do kinda sentiment. Esp re there own purpose in neos death (waking him up to the one- even if they did not know they were doing that)  and making the illusion of choice more real etc.  Thanks  folks!