Season synopsis
Contains spoilers for this season and earlier seasons.
Fourteen years after the X-Files were closed, FBI Assistant Director Walter Skinner brings Fox Mulder and Dana Scully back together to meet online broadcaster Tad O'Malley. They hear Sveta's account of alien abductions and see a craft built with extraterrestrial technology. Mulder now suspects that government figures used alien technology to stage an invasion story and conceal experiments on people. Before O'Malley can broadcast the evidence, armed men destroy the craft and its research site, and a UFO intercepts Sveta. Scully's independent tests find an unexplained, apparently extraterrestrial element in both Sveta's DNA and her own. The agents reopen the X-Files with a changed theory of the conspiracy, while the Cigarette Smoking Man learns that they are active again.
Their renewed work also sends them through cases beyond the conspiracy: a Department of Defense scientist's suicide exposes a secret mutation experiment; a body in the woods may point to a creature; and an apparently impossible murder of a city official coincides with a personal loss that revives Scully's grief over the son she placed for adoption. When two younger agents ask for help communicating with a comatose man involved in a terrorist attack, Mulder and Scully guide them through the case. Six weeks after the reunion, a fast-moving epidemic overwhelms hospitals. Monica Reyes tells Scully that the Smoking Man offered her a place among the planned survivors. Scully searches for a cure using the DNA that protects her, while Mulder refuses the Smoking Man's offer and collapses from the infection. Scully says William's stem cells may save him; a triangular UFO descends over them, and the season ends before their fate is shown.