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That is the oracle.........when Neo/Smith was destroyed all the bodies that Smith had copied himself into returned to normal. That was the Oracle's body that Smith was inhabiting while fighting Neo. When Smith was destroyed, the body went back to being the Oracle. That is why she was laying in the pit.
Neo is part machine.........this is a big focal point of Revolutions. He is connected to them....just as any other machine is. This is why he can sense them, destroy them, and even see them when he is blind.
What happens to a program inside of the Matrix when it is destroyed? It returns to the source........or escapes and hides in the Matrix as an exile. I assume that Neo was headed for the source after being destroyed...........remember the prophecy about Neo entering the source and bringing an end to the war? ......exactly.