Except that it wasn't. The Smoking Man was an extra, known in the script only as, you know, "the Smoking Man." His entire purpose was just to stand around in the background whenever the writers wanted to remind the audience that Mulder and Scully were being watched by somebody. If you don't know what we mean, go look at the IMDb page of the actor, William B. Davis. Before his 1993 casting in The X-Files, he was playing roles that didn't even get actual names -- he played "Judge" in an episode of MacGuyver, "Doctor" in one episode of Nightmare Cafe, and "Lawyer" in the TV movie Omen IV: The Awakening. And who could forget his work as "Inspector #2" in that one episode of Wiseguy?
So why would the producers of The X-Files declare this random background actor to be the central villain of the show's overarching storyline involving alien beings, government coverups, and unresolved subplots? They even did an entire episode joking that Cigarette Smoking Man was behind pretty much every terrible world event of the last 40 years. The answer is that the writers never intended for that to happen at all.
Another conspiracy sadly debunked.
As we've pointed out in the past, the central plot of the show was more or less made up as it went along. It was only when Gillian Anderson got pregnant and took a partial hiatus from the second season that the writers needed to introduce new characters to make up for her absence. Davis was given a speaking role for the first time, and that's when the creators of the show suddenly realized, holy shit, he can actually act. They had stumbled across an iconic Hollywood villain by getting lucky with their extras casting.