This question already has an answer here:
I just finished The Matrix Reloaded. Not for the first time, though this run through of the trilogy is very enlightening. Every piece of it makes sense to me so far except at the end. When The Neb is destroyed by the bomb sent by the machines, the machines attack Morpheous, Trinity and Neo. Neo then destroys them with some kind of EMP like attack. How is this possible? How do his powers exist outside of the Matrix?