The episode opens "in medias res" in 1989, when a SWAT team conducts a raid on a Baltimore warehouse. Inside, they find a naked and disoriented Fox Mulder in a box, shouting, "They're here!" Three men attempt to flee the scene and are captured; they are revealed to be the Lone Gunmen. As they sit in a city jail, they begin blaming each other for the predicament they have found themselves in. Detective John Munch interrogates John Fitzgerald Byers, who tries to explain what happened.