When the second X-Files movie was released in 2008, it completely ignored the overall mythology and didn't address the colonization plot in favor of telling a monster of the week-style standalone story. The plan at the time seemed to be making a third film to address the issue in 2012, but a follow-up never came close to materializing.
News of a revival coming in 2016 gave hope for a wrap-up to the alien colonization plot thread. Unfortunately, as seen in seasons 10 and 11, a satisfying one never really came.
In the "My Struggle" series of X-Files episodes, it's revealed that the Cigarette-Smoking Man and some of his surviving Syndicate conspirators have embarked on a plan to use an alien virus to depopulate the Earth.
In "My Struggle III," Mulder encounters a mysterious man referred to as Mr. Y and his associate Erika Price. They seek to stop CSM's plan and want Mulder's assistance in doing so. During their interaction, Mr. Y and Price reveal that the aliens called off their colonization plans at some point before 2012, due to having "no interest in a warming planet with vanishing resources."
Hardly a great explanation? With the advanced technology, would a simple loss of resources and an increase in temperature dissuade aliens from such a long-held goal of colonizing Earth? At the same time, there weren't many options for how Chris Carter could write himself out of an apocalypse which has already occurred before Season 10. Maybe they never meant 2012 to come and go without a resolution to the colonization story. Presumably, Mulder and Scully preventing it somehow. Then again, there's always the possibility that Mr. Y and Price are lying...
Source: Screen Rant