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The instruction manual for Mega Man X contains "The Journal of Dr. Cain", in which the story leading up to the events depicted in the game is narrated through excerpts of Dr. Cain's personal journal. According to the journal, Dr. Cain, an archaeologist searching in the year 21XX for fossil records relating to Mesozoic plant life, accidentally discovered the ruins of a robotics research facility that had once been operated by the legendary robot designer Dr. Thomas Light. Among the ruins, Dr. Cain found a large capsule which contained a highly advanced robot the likes of which the world had never seen before. This robot, Mega Man X, had human-level intelligence and emotion. Fascinated by the genius of Dr. Light's design, Dr. Cain studied X and Dr. Light's few remaining notes. With X's help, some months later, the first "replicate android" or Reploid (in Japan, Repliroid), a robot who can think, feel, learn, and grow exactly like a human, was made. Within the year, the design had been standardized and Reploids were being mass-produced.
However, with the free will given to a Reploid came the possibility of criminal activity previously unknown to robots; such rogue Reploids were said to have "gone maverick" and were later referred to as Mavericks (in Japan, Irregulars). As the public outcry against the few Maverick incidents became too great to deny, the government stepped in, and under the advice of Dr. Cain, formed an elite military police organization called the Maverick Hunters. The Hunters would capture or disable any Reploids that posed a danger to humans, provide damage control at Maverick uprisings, help with disaster recovery, and perform other tasks as needed.
For the leader of the Maverick Hunters, Dr. Cain designed a very special Reploid, one with a very advanced thought system. This Reploid, thought to be immune to whatever defect of manufacture, design, or social conditioning caused Mavericks, was named Sigma. Sigma headed the Hunters for about three years before the very head of the Maverick Hunters himself became a Maverick, taking the vast majority of the other Hunters with him. Sigma seized control of a small island and drove all human occupants out. Claiming that the humans were "inferior" and that they were limiting the growth and potential of Reploids, he called for his followers to begin a massive extinction effort. It seemed, with only one remaining Hunter able to fight (the mysterious Zero of Unit 17), that all would be lost and human extinction would become inevitable. But X, guilt-ridden at having helped design such a ruthless and warlike race, decided to join forces with Zero and attempt to stop Sigma at any cost.