MULDER AND SCULLY FIND AN UGLY TRUTH FROM THE PAST--AND THE PRESENT--HIDDEN IN AN ABANDONED MINE, WHILE SKINNER AND THE CIGARETTE-SMOKING MAN BARGAIN FOR THE AGENTS' LIVES.
Agent Scully and Assistant Director Walter Skinner, deadlocked in an armed stalemate, are equally shocked when Mulder, whom they thought dead, stumbles into their midst. Skinner reveals that he has the missing DAT tape given to Mulder by The Thinker, and offers to bargain for their return to the FBI. The Cigarette-Smoking Man reassures the Well-Manicured Man and his cronies that Mulder is dead, but the Well-Manicured Man demands the tape. The Lone Gunmen help Mulder and Scully find an ex-Nazi scientist who claims to have known Mulder's father. He directs them to an abandoned mine where they find a vast filing system containing detailed medical records on millions of people--including Dana Scully and Samantha Mulder. The Well-Manicured Man, alerted by the Nazi scientist to the fact that Mulder is alive, despatches a hit squad. Before they arrive, Mulder witnesses the takeoff of a craft unlike any on earth, and Scully sees a crowd of what may be aliens rushing past her. They follow the aliens out a secret exit, escaping the Well-Manicured Man's trap. They agree to Skinner's offer to negotiate a deal for their safety, but when Skinner stops at the hospital where Melissa Scully is lying in a coma, Alex Krycek ambushes him and steals the tape. Deception piles on double-cross as events build to a tense confrontation between Skinner and the Cigarette-Smoking Man. The latter, knowing Skinner has no tape with which to barter, sneers at his offer, until Skinner reveals the ingenious means by which the contents of the tape have been shared and secured. Finally, in a poignant moment at Melissa Scully's bedside, Mulder and Scully share a reaffirmation of their faith in one another and their quest for the truth.