matrix theory
I think the major point that people seem to have over looked here is that Zion is obviously a sub program set into the matrix to control the inevitable anomaly (neo) as said by the architect, this explains the fact that neo was able to stop the sentinel in “the real world” and also that smith is now in “the real world” and was responsible for the destruction of all the ships via the early activation of the E.M.P, also the architect tells neo that if he goes through to the source he will be responsible for rebuilding Zion true but, it is a different Zion he is building, if he goes to the source he is released from the matrix to another sub program with 25 others and the matrix is left untouched (what reason do the machines have to destroy there power source if the one is eradicated) however because he chooses to remain in the program to save trinity there is now the new problem that the anomaly is not only still there but knows what’s going on.