Despite his horrifying injuries, CSM survived and was recovered by associates of his and taken to a hospital where he received prosthetics and was expected to make a full recovery. Shortly after the closure of the X-Files once again CSM called upon Monica Reyes who came to see him in his hospital room. Having now been back in with the conspiracy and helping overseeing a plan for depopulation of the human race, CSM made a deal with Monica to work for him in exchange for her life. She reluctantly accepted, left the bureau and disappeared. Over the next fourteen years the Smoking Man would be presumed dead while he and an unknown group of associates started putting their scheme into place. — (MY STRUGGLE II)
In 2016 he received news that the X Files had been reopened. — (MY STRUGGLE)
The CSM was the leader of a plan that was involving wiping out a large part of mankind, as they were destroying the planet slowly with their way of life, a destruction which was foreseen by the aliens years ago. It is unknown if those aliens intended to colonize the planet after having wiped out humanity.
For that plan to succeed, the Spartan Virus, a virus which would deactivate the immune system in any human infected, was given to the people via the Smallpox vaccine since 2012. After millions of people died of generic disease, the world would start over with an elite in control, an elite that was given alien DNA to protect themselves from the Spartan Virus. This kind of hybridization may have been the goal of the Syndicate before its destruction, however it is unknown how it was achieved. — (MY STRUGGLE II)