Agents Mulder and Scully return after 13 years to investigate a government conspiracy at the behest of a popular web-TV-show host, who introduces them to a woman who claims she's an alien abductee and shares startling news with them.

The season concludes with people all across the country falling gravely ill. A widespread panic develops and Scully looks within to find a cure. Meanwhile, Mulder confronts the man he believes to be behind it all, but another figure from Mulder and Scully's past may prove to be the key to their salvation.

Mulder and Scully rush to find an on-the-run William while the Cigarette Smoking Man pushes forward with his ultimate plan.