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The Matrix History and Background
"I was startled to discover that my entire life consisted of nothing more than a sequence of zeroes and ones."
--Binary

...excerpted from

ENCYCLOPEDIA HUMANICA
VOLUME XXXII
CHAPTER 13
ZION AFTER THE SECOND RENAISSANCE

FORWARD
A Summary of the Development of Zion and Discovery of the Matrix

Following the war against man and the Second Renaissance, surviving members of the human race were driven deep into the bowels of the earth.  Humans themselves were admittedly partly at fault.  In an attempt to deprive the machines of their primary energy source, the sun, humans had set off devices around the globe to cut off all sunlight.  The machines turned to the best alternate source of power they could conceive of--a limitless source of renewable power--by harvesting humans.  This drove survivors into pockets within the crust of the earth, miles below the destruction and danger above.

As the survivors gathered and organized themselves, they started production of a great city.  Zion, they called it, the last hope of humankind.  They formed a city government, a council, and appointed a man known as the Philosopher as their leader.  They sent patrols to the upper crust to search for survivors and steal machine technology.  They assumed that the harvested humans were unaware, in a coma-like state, and efforts to release them resulted in death.

Then they found the man known as Binary.  They could tell immediately from the jack-slots in his head and body that he was a harvested human.  He told them of the alternate reality, coined the Matrix.  He told of his position as a top programmer in the U.S. government within the Matrix, and of his discoveries that would allow others to escape the Matrix and the domination of the master computer, Zero-One.  

Within several years, Binary and the Philosopher devised of a way to jack into the Matrix and retrieve more humans to join Zion.  Ships were stolen and EMP devices refined to keep Zero-One at bay during these search and retrieve missions, and a core contingency of soldiers and volunteers brought from the Matrix were sent back in.  The hope was that they could:  (1) find some way to destroy Zero-One and the Matrix to save humanity, and (2) bring back harvested humans willing to join the small community at Zion and the "real world."

...

That was three years ago.  The HRP ("Human Retrieval Program") is still in its infancy, and you are part of it.  Despite best efforts, there have been less than forty successfully revived humans, and there are still less than fifty thousand strong in Zion.  Yet these are the last and best hope for mankind.