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Much of the Matrix is based on Biblical Story. One of the most central themes is the Fall of Man - i.e. man being kicked out of the Garden of Eden.
In the original Matrix movie, Morpheus is told by Agent Smith that this Matrix he knows now is not the original Matrix. Smith explains that the very first Matrix created by the machines was actually a wonderful paradise, full of peace and love.
Smith says that mankind rebelled against this world, and could not live in it. They found it too unnatural, and could not accept it.
Mankind therefore, directly because of his own actions, had to live in the "real world" we know instead, full of war, hate, love, jealousy, envy, and all the rest of it. They wanted the choice to do whatever they wanted, whether it was for good OR bad.
Yet man still dreamed of a Messiah that would come and save him from this world, and bring him to a state of peace. In real life, that messiah would be Jesus Christ (if you are Christian), a future Messiah (if you are Jewish) or other chosen individuals for other religions. For the Matrix, that hoped-for Messiah is Neo, working with his ever-faithful friends to help mankind escape from the harsh world they are in and move on to a better life.
These Biblical themes become even more explicit in The Animatrix: The Second Renaissance Part I which tells the back story of the Matrix amidst Biblical quotes and obvious references. In one scene, a male and female walk up hand in hand, and the female is holding the apple!
The Matrix Reloaded: Review
The Matrix Reloaded Cast Listing
The Matrix Reloaded: Plot and Spoilers
The Matrix Reloaded: Posters and Images
The Matrix Reloaded: Zionism and Judaism
The Matrix Reloaded: City of Zion
The Matrix Reloaded: Persephone in Mythology
The Matrix Reloaded: Merovingian in History
The Matrix Reloaded: Thadeus in History
