Cigarette Smoking Man/Post-Syndicate

In October 1999, the CSM was present at a meeting which discussed an upcoming crisis somehow involving Agent Mulder and Scully's recent discovery of an extraterrestrial artifact. 
Soon after, the CSM visited Mulder in the hospital after the artifact had made Mulder immune to the black oil. He took Mulder from the hospital to a laboratory and had him sedated in order to extract genetic material from Mulder. This was an attempt to make himself immune, even though there was a chance the procedure would kill Mulder. Fowley was with him, and the CSM convinced her that he would take Mulder's burden from that point on, giving Mulder a "hero's death." The operation completed successfully and he left As a direct consequence of his attempt to infuse himself with hybrid DNA, the CSM slowly began to die from cerebral inflammation. By the next summer, he became wheelchair-bound and had undergone a tracheotomy, which may have resulted from cancer as predicted by Jeremiah Smith. 
In 2000, the CSM found out that Scully was looking into the investigation into Samantha's disappearance. He entered her apartment and waited for her. Then, he told her that he indeed called off the search for Samantha because she could only be dead. When Scully challenged him, saying why let Mulder think she was alive, he explained it was what gave him hope. 
The CSM got word that a scientist working with alien technology at wanted to distribute genetic research so that it could be used to the benefit of all. He decided to use Scully's identity to lure the scientist into the open. Calling himself "Cobra", the CSM gained his trust over a few months using Scully's email address and her computer. When it came time to bring Scully in, he saved a boy with cancer, Jason McPeck, and lured Scully and Mulder to the situation. When Scully alone went to investigate, the CSM made his offer in private of the research that saved not only the boy but would cure cancer for everyone, under the guise that he wanted to "make right." He also insisted that Mulder not be told. Later, in an office, he was pleased to see Scully would take up his offer. He set up a trip for the two of them, insisting that it would take time and that he was working under the radar. However, he had the BHM tail them and make sure Scully did not tip anyone off. He waited for her at her apartment and they left together. After a long drive they arrived at a house at 1AM in the morning in Milford, PA. He brought her inside and changed her clothes, which would make her furious the next morning. She almost left, but came back for the larger mission.
The CSM brought her to dinner to meet Cobra and, during, told her that the research was cure for all human disease, not just cancer. He said cobra wanted assurances that the science wouldn't be used for evil purposes. He left to smoke and meet the BHM, who confirmed that Cobra had not shown. However, he learned on his return to the table that Cobra had left a note. The next day, he let Scully go meet Cobra in a boat alone. He watched as BHM killed Cobra, but the CSM killed BHM just then rather than let Scully be killed. He let her go with a copy of the material (really a blank disc). Later, he took the real copy and threw it in the lake, confident it would not resurface. 
In June 2000, after a UFO crash in Bellefleur, Oregon, the CSM attempted to rebuild the project. He had Covarrubias rescue Krycek from the Tunisia prison to investigate and retrieve the UFO for him. While he was gone, he confided to Covarrubias that he knew how to find the alien ship, but didn't trust Krycek and wanted him to prove that he could do it.
However, Krycek was unable to retrieve the UFO, and instead returned to the CSM's apartment empty-handed with Covarrubias. The CSM deduced that he never intended to succeed and, indeed, Krycek attempted to kill the CSM by pushing him down a flight of stairs. 
The CSM survived his fall, and went to live in the magnetite pueblos with a group of Native Americans. He became a wise man in their tribe. In May 2002, the CSM sent Mulder, who was in hiding in New Mexico, a key to the Mount Weather Complex in Bluemont, Virginia. The CSM was later seemingly killed by black helicopters sent to kill Agents Mulder and Scully. 
===Depopulation scheme===
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 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. 
In 2016 he received news that the X Files had been reopened. 
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. 
The CSM planned to find Scully's son William, as he needed him for his plans and wanted to prevent another group getting to him first. He secretly tapped into the phone of his son Jeffrey, who had been hiding William and got attacked by a man trying to find out where William was. CSM informed Monica that Mulder will come after him and try to kill him.
When Skinner gets into his car to go look for Scully, he is held at gunpoint by Monica (although he grabs it off her and turns it on her). CSM gets into the car and offers Skinner a deal to join him and survive the mass extermination of humanity in return for his help finding William. However a disgusted Skinner refuses, and CSM reveals that Scully herself will survive when the end comes. After Monica leaves the car, the CSM is forced to remain with Skinner. The CSM reveals the truth of William's parentage; that he is the father due to artificially impregnating Scully using alien science, a revelation which shocks Skinner. 
While pursuing the whereabouts of his son, William, he constantly keeps in contact with Skinner, demanding that he bring him the boy. Finally, the two would cross paths later when Skinner drove Scully to Mulder's location (which happened to be William's as well). Skinner and Smoking Man come face to face. CSM himself was stuck on the passenger seat of the car, with Monica at the wheel. Skinner slowly walks toward him. Finally, when Skinner draws his weapon, CSM steps on the gas. Monica tries to stop him, but is unintentionally shot by Skinner. CSM continues to ram the car into Skinner, but not before Skinner drops to the ground.
He gets out to see that Skinner is either dead or unconscious, so he grabs his gun and continues to pursue William.
Not long after the showdown with Skinner, he comes face to face with Mulder at the edge of the docks. While aiming his gun at his first born son, Mulder (actually William disguised as Fox) comments that he believes his own father wouldn't shoot his son. CSM continues saying that he shot his second son (Jeffrey Spender) and shoots Mulder through the head.
To his surprise, he hears Mulders voice coming form behind him, who proceeds to fire multiple rounds into his father's chest. For a few seconds, Mulder looks CSM in his eyes and then proceeds to push his body off the pier and into the waters below.
Mulder watches as his father's lifeless corpse is slowly dragged away by the rough waters, ending the Smoking Man's schemes for good. 
===Illusory versions===
In an attempt to communicate with a comatose terrorist in another plane of existence, Mulder was administered what he thought to be psychedelic mushrooms by Agent Einstein (which actually placebo pills), which sent Mulder into a drug trip. During this trip he found himself on a rowboat, where a hallucination of the Smoking Man whipped Mulder, informing him that he came to the right place in order to find out the truth. The Smoking Man disappeared and Mulder proceeded to communicate with the terrorist who was present on the boat. 
In a premonition experienced by Scully in which the CSM's plans were put into motion, Mulder confronted the CSM and demanded he stopped what he was doing, but CSM told him it was too late. The CSM said he didn't want Mulder to die and wished for him to join his elite and offered him the cure, but Mulder refused. Mulder then collapses, still refusing the CSM's help.
Agent Miller comes and saves Mulder, but the CSM tells them that nothing can be done for anyone. 
Category:Cigarette Smoking Man