The man behind the cloud of smoke seems to constantly have his hand in the affairs of the X-Files, and his presence serves as a warning that the shadow government is using Mulder as a pawn in their game.
The tension between Mulder and the Cigarette-Smoking Man has steadily increased as the man with the pack of Morleys not only involves himself in Mulder's work, but also has been responsible for several attempts on the agents' lives. In "One Breath" (2X08), Mulder blames CSM for the abduction of Scully, and comes within a trigger-pull of killing him. But Mulder later learns that the CSM has connections with Mulder's parents and was a major player in his sister Samantha's abduction.
Mulder and Scully uncover his real name, C.G.B. Spender (although this too may merely be another alias), when they learn that his ex-wife is abductee Cassandra Spender. The CSM had his son Jeffrey assigned to the X-Files after Mulder and Scully are taken off the unit, but young Agent Spender proved a disappointment to his father. The CSM ultimately kills off his own son in "One Son" (6X12).
In "The Sixth Extinction: Amor Fati" (7X04), Mulder's alien DNA is transferred to the CSM in order to make him a hybrid. But the procedure caused a cerebral inflammation in the elusive smoker. Although the old man is already dying, his former mercenary, Krycek, tosses the CSM down a flight of stairs in "Requiem" (7X22).