In this continuation of the previous episode... A team of camouflaged soldiers, lead by The Cigarette-Smoking Man, searches for Mulder and the computer tape believed to be in his possession. Albert Hosteen and his family are interrogated and beaten, and Scully-whose visit to the smoldering boxcar produces no leads-is detained, searched, and questioned. But the Cigarette-Smoking Man's efforts are in vain.
     At F.B.I. headquarters, Scully is given a mandatory leave of absence until a review board investigates the nature of her insubordination. Crestfallen, Scully returns home to her family. She tells her mother she erred by countermanding her superiors. When Scully returns to Washington, Frohike informs her The Thinker-the computer hacker who accessed the MJ files-was professionally executed by unknown assailants. When Scully approaches Skinner with the news, and theorizes how Mulder and The Thinker could have been gunned down by the same individuals, Skinner shows interest only in the missing computer tape.
     Meanwhile, Albert and his family investigate when buzzards begin circling high above the New Mexico desert. They find Mulder's limp, lifeless body near a tunnel in the red rock quarry. He is transported to a Navajo hogan, an igloo-like dome of mud, where a healing ritual called The Blessing Way is performed over his body. As the ceremony progresses, Mulder's soul encounters a bridge spanning two worlds. He encounters visions of Deep Throat, and his father, and of the aliens trapped inside the boxcar. On the third day of the ritual, the Navajos watch as Mulder regains consciousness.
     While passing through a security checkpoint at FBI headquarters, Scully sets off a metal detector. A security guard waves a magnetic wand near her neck and again trips the security alarm. Puzzled, Scully visits the medical lab, where a physician removes a computer chip from beneath her skin. Melissa convinces her sister to visit Dr. Pomerantz, a hypnotist. While under hypnosis, Scully encounters repressed visions of men, lights and alarms.
     Having recovered from his close brush with death, Mulder returns to his mother's home in Martha's Vineyard. He searches for clues about his father and the people he worked with, certain they will lead him to his missing sister.
     While attending Mr. Mulder's funeral, Scully is approached by a Well-Manicured Man. The stranger claims Mulder is dead, and that a hit squad is out to kill her. Later, Skinner approaches Scully outside her apartment. The pair drive to Mulder's apartment, where a very suspicious Scully pulls out a revolver and demands Skinner answer her questions.
     Searching through Scully's darkened apartment, Alex Krycek and his assistant encounter Melissa. A shot rings out and Melissa slumps to the floor.
     As the standoff between Scully and Skinner continues, someone approaches the front door to Mulder's apartment. Catching Scully off-guard, Skinner pulls out a gun.