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The Plague is a result of the nanotechnology experimentation conducted by the Ultor Corporation and, more specifically, Dr. Capek. The disease was featured in Red Faction.

Progression
Though the exact nature of the Plague is never explained in the game, fans have speculated about its progression.

The Plague results from human exposure to nanites created by Capek. It is thought that when such nanites enter a human body, they begin to attack the brain. The attack stops all non-essential neuro-muscular functions, causing the victim to fall to the ground and making them unresponsive.
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