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Morpheus was the captain of the Nebuchadnezzar, a hovercraft of the human forces of the last human city, Zion, in a devastated world where most humans are grown by sentient Machines and kept imprisoned in the Matrix, a virtual computer-generated world.
Since Morpheus, as a hovercraft captain, possessed access codes to the Zion mainframe computer, the surviving members of the ship's crew were about to unplug Morpheus from the Matrix without the ability to retrieve his mind for his body, a process that would kill him.
Morpheus was barely able to escape the treatment facility; however, upon escaping, the Assassin bent the code of the Matrix and emerged from a vent in the wall.