smith trapped inside neo body

Here a possible an i do mean a possible theory, maybe when smith copied himself into neo, the deus ex machina used neo's body as a continer to trap smith and thats why they took him away, to destroy or study how a matrix program effect a human living body.

New form of control (using human bodies that have matrix programs in them to control the humans of zion)

I thought it was to provide a connection between Smith and the machines allowing Smith to be deleted.

Smith no longer had a connection the to machines when Neo jumped into him in M1. This is apparent in M2 when Smith returns his earpiece as a gift to Neo for "setting him free."

they've said throughout the movie....when a program faces deletions.....it either goes to the source....or chooses exile...well smith chose exile after M1 and in M2....Neo was at the source....in M3 when he copied Neo...Smith had then reached the source and they deleted him.....

No matter how wierd that sounds, it seems like a good theory......................

(the first part though, i'm not too sure about the control part)

Neo and Smith are opposites. In a mathematical equations you cannot have both in the same spot. Neo realized that the fight would go on forever. He had to scrafice himself. When Smith took over Neo's body they have to cancel each other out and that is why all of them died. But that is just my opinion.

XXf ManXX, i neverd heard that theory,but i like it, i think ur right.....