At any rate, my predicition, The Matrix is simply a program inside another Matrix. We will find that Neo is in fact Human, but everything around him (morpheus, trinity, Zion) are all programs and designed for the simple purpouse to help the "architect" to better learn Human's and create a Matrix that can better imprison Humans. Neo is recycled back into the Matrix for further study, or, breaks out and is alone (the last part I'm not sure of yet..)