Originally posted by dubkatz: The machine didnt work thru neo....
The machines did work through neo. That was part of the deal to stop the war, which is why he went to the machine world. Smith was getting too strong for anyone to control so made a deal that would allow himself to be used as a conduit for the machines to destroy smith, while sacrificing himself in order to help the machines and save zion. That's why when smith assimilated neo at the end, he said 'it's a trick' and then the machine that neo was 'plugged' into sent the virus or whatever it was through neo in order to infect and destroy all the smiths.