The X-Files revival was hit or miss among fans and critics alike, with the majority of criticism hurled at the played-out mythology. While Season 11 delivered some strong Monster of the Week episodes, "My Struggle IV" was declared a disappointing wrap-up by many. William's status as Mulder and Scully's son was abandoned when the Cigarette Smoking Man (CSM) revealed himself as the father of Scully's superhuman child. This, understandably, didn't sit right with audiences who had long believed Mulder was William's true father. Coupled with the lack of respect for Scully's character and autonomy, many fans have rejected CSM's claims altogether. However, looking back at a Season 7 episode shines new light on what has become The X-Files' biggest controversy.
Source:https://www.cbr.com/x-files-mulder-scully-son-theory/