Fox initially hoped for The X-Files season 12 but it never happened. After spending nearly a decade investigating paranormal phenomena and the existence of extraterrestrials in the 1990s, David Duchovny and Gillian Anderson took a well-earned break. Agents Mulder & Scully then returned for a revival in 2016. The ten-episode The X-Files season 10 was an absolute hit with audiences, so Fox ordered another season which aired in 2018.
The X-Files season 11 picked up directly from the previous season as Agent Mulder and Agent Scully searched for their son William. However, it wasn't so simple. It turned out season 10's ending was one of Scully's visions that hadn't happened yet, while the Cigarette Smoking Man was revealed as the father of Scully's child, not Mulder. The season 11 finale ended on a plethora of cliffhangers: the superpowered William was shot by Cigarette Smoking Man yet by the end of the episode looked very much alive; Scully announced that she was pregnant with Mulder's child.
These plot threads currently look to never be resolved as, in the months following the end of season 11, Fox announced that they had no plans for The X-Files season 12. Initially, the network claimed the decision for an indefinite hiatus came from Anderson, who had decided she was done portraying Dana Scully prior to the release of The X-Files season 11. Anderson has since clarified the statement, revealing that her exit might have nudged the cancellation but the real reason for no season 12 was the decrease in viewership.
When The X-Files was revived in 2016, the first episode had the highest viewership numbers for the series since 2001. The ratings remained steady for season 10, averaging over 13 million viewers which made it the seventh most popular TV that year. By the end of season 11, viewership dropped dramatically, which was enough to hit the breaks on the series.
Series creator Chris Carter initially stated that he believed that The X-Files could survive without Scully, but he later changed his tune. Like most viewers, he would have a hard time imagining The X-Files without Duchovny and Anderson (indeed, the show had stalled the first time following Duchovny's reduced role). Whether or not the decreasing viewership figures played a role is unclear.
Many long-time viewers of The X-Files weren't too pleased with how season 11 ended. Anderson similarly shared her discontent with the storyline. Carter is holding out hope that Anderson might change her mind in the near future, although that doesn't seem likely. The X-Files has run its course and it's best to follow in Anderson's footsteps and let it go. There are always opportunities for spinoffs or other projects but the truth is no longer out there for Mulder and Scully.