The writers of this movie want you to ask yourself what you believe and what is the controlling factor behind it all. Finally throughout the movie are fatalistic vs. controlling your own destiny motifs. The greatest messiah image of The Matrix is the final scenes. These are the Passion Stories retold. A sentinel empties his clip into Neo.
All hope is lost.
The crew of the Nebuchadnezzar mourns. Trinity is broken-hearted and the Trinity of Father, Son, Holy Spirit is broken. Neo, however, is resurrected. He is the One. After his revival, he sees things in a new way, has new powers.