After the collapse of their relationship, former FBI agents Fox Mulder and Dana Scully are reunited by a TV host who promotes conspiracy theories about the government and believes that alien abductions are actually false flag operations.

A scientist working for the DOD commits suicide. Mulder and Scully start an investigation only to discover a secret mutation experiment.

Mulder questions his faith in the unexplained. He attempts to gather proof of the existence of the new creature he and Scully investigate before jumping to conclusions.

Scully receives bad news about her family while away on a case. Mulder finds a strange paint sample at the crime scene which leads him to the left-handed artist that created the main suspect. This brings back memories to Scully.

When a terrorist ends up in a coma, a pair of younger FBI agents ask Mulder and Scully for help communicating with the man, resembling them when their adventure first began and reminding them of just how far they have come.