this is the most prominent scene when thinking about that:
https://www.youtube.com/watch?v=Q-VPKuKvOvc
here Neo asked directly why he can do all that things even when not plugged into the matrix. the oracle gives him a very loosly coupled, unspecific and lousy answer. but it MAY point at that theory, that the „reality“ (zyon, outer world, etc) is a second layer of the matrix. we never got any real explanations for Neos abilities (like „seeing the source“ when he becames blind, stopping machines, etc) in the real world, beyond that talk between him and the oracle.
given the fact, that a machine can not lie and the architect told the full truth, the matrix lacks by an unsolved mathematical term. both parts of that math term are Neo and Agent Smith. Neo just exists, as some „outside of Agents Smith control“ logic, to reboot the Matrix and therefore delete Smith. This can be just done from the „outside“ because Smith controls everything inside, after a while. so, if you are a machine and you have to eliminate that term/problem, you would do exactly that.
that said, 2 thoughts come up:
1)
if Neos „outside“ is really the reality, how to control Neo and make sure he reboots the matrix ? also if the outside is the real reality, what are Neos abilities then ?
2)
if Neos „outside“ is not the real reality, but a second layer of the matrix, it solves all questions in point1. but it raises 2 new questions:
- how you make sure, Smith is not also controling of, or gaining access to, layer2 ?
- why you need Neo, when you can just reboot Layer1 from Layer2 ?
the second answer is solved, when Neo just IS exactly that mechanic. a program that think it breaks out (from layer1) and reset layer1 from layer2. a layer2 (and Neo as a program), that cant be reached by Smith. but above first question (how make sure Smith cant control Neo or reach Layer2) still exists.
so, i am not sure here. but its somewhat a possibility.