As soon as Neo stopped the sentinels at the end of M2, your typical audience member theorized that the real world is just another Matrix. However, this theory doesn't reconcile with a few details in the movie. For support of this, see Debunked: Matrix Within Matrix.
Depending on which power you look at, Neo's powers are enabled by a variety of things, which include his anamalous summation (powers within the Matrix), the Oracle (visions of the future), and a connection to the Source (powers in the real world).
| Neo's Powers: Back to Life Neo's Powers: Vision of Future Neo's Powers: Stop Sentinels Neo's Powers: Blind Sight |
 Conversations: Neo & Oracle (M3) |  Neo's Powers: Back to Life |