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I just want to know for sure that the smith virus infected everyone, right?

Why didn't the oracle go to the architect's safe-place in M3? I mean she is the mother of the matrix right?

In reloaded, during the fighting scene between the smiths and Neo right after Neo's talk with the Oracle, did smith really assimilated that agent that appeared or did smith just assimilated the woman? In other words, did that agent just died or did he simply transfered somewhere else?

smith is a virus (of a certin sort, he has more meaning then a simple multiplying virus) as well to answer your question, no the "agent" who got taken over did not die only the woman (also the people dont "die" you can see this because in the freeway scene all 3 agent are there in the scene......hope this helps.........!

its said that the smith program is out of control - when they blow up at the end the yellow/white explosions continue through the whole city so i think he assimulated pretty mush everyone.

dont know about the agent/women question - is that particular agent seen again in either M2 OR M3?

well that solves the agent question then!