He just took over Keanu's body when Morpheus get him out of the Matrix.
The Matrix is trying to screw his mind using the architect. Stopping Neo from trying to save Zion. There is no #1,#2,#3...
The bodies providing the Matrix should have been genectically altered by the Matrix (e.g. the plug at the back of the head) making them (Neo, Trinity, etc) somewhat of a cyborg.
Pt 4 could have given Neo certain communication channel (RF) to sense the sentinels.
- Could someone please post the speech by the architect?