Mulder returns from Hong Kong with Krychek in tow. However, they are attacked by unknown agents and Krychek manages to escape while Mulder finds himself in a hospital. Meanwhile, Skinner is also admitted to the hospital suffering from a gunshot wound fired by a man who is working for the group that wants Scully's sister's murder investigation to end.

Cyclops heads solo to the desert town of Skull Mesa, where humans and mutants live in harmony, to visit an old mentor from his youth. But he not only finds himself powerless when he arrives, but discovers the place under the rule of a maniacal mutant, with none of the citizens willing to take a stand.

Following his breakdown, Daniel returns to work but doesn't feel the job is suitable as a vigilante attack takes place resulting in an elderly man having a heart attack.