Mulder and Scully have 24 hours to save Assistant Director Skinner from being killed by a biologically engineered disease. The disease appears to be created by a shadowy government organisation but in order to save Skinner's life; they must determine who wants him dead, and why. With Skinner's condition worsening Mulder seeks assistance from Senator Matheson who he hopes can provide some answers and help him to find a cure.

While Cigarette Smoking Man recites to an unseen listener everything about the work of the Syndicate involving a global conspiracy in co-operation with an alien species, Cassandra Spender reappears and is pursued by the scientists who would rather kill her than keep her alive. Cassandra runs to Mulder's apartment and demands that he shoots her because she is the culmination of 50 years work - a living alien/human hybrid, and colonisation will begin if the aliens find out about her.