Originally posted by JediHDM
just thought of another example. Michael Popper. He self-substantiated. he freed his mind without Neo or Morpheus. Thus, his mind was put back into his body. However, his family had a funeral. there had to be a body, as they knew where he died. If his mind is in his body, as it has to be for him to be alive, then what was left was not his mind, but rather, a shell, a body for his mind. it is not his mind though.
The answer is in when the Logos flown by Trinity was flying to machine City and you see the fields where the babies are grown, glowing from the Source.
If you are hooked up to the matrix and die in it, you wake up in the real world. It is when you are flushed from your pod that you drown because your muscles have atrophied so you can't swim and your body eventually reaches the processing plant where the body is then liquified to feed the living.
Except in Neo's case as with Karl Popper they were watching for his body and intercepted it in time.