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Scully helps Mulder to fake his own death in an effort to discover which members of the FBI they can trust before the agents individually search for an answer to Scully's cancer.
Beginning 24 hours before the last scene of the previous episode, a distraught Fox Mulder sits in his apartment. He receives a phone call from Michael Kritschgau, who tells him that 'they' may be listening. Mulder, spotting a small hole in his ceiling rushes upstairs and bursts into the apartment above his. Inside he finds Ostelhoff burning phone records. When Ostlehoff reaches for his gun Mulder shoots him. Mulder meets Dana Scully (played by Gillian Anderson) at her apartment, telling her that Ostlehoff was a Department of Defense employee spying on him for at least two months and he now lays dead in his apartment. He also reveals that the phone records he was burning show numerous calls made to the FBI.The next day Scully heads to Mulder's apartment and identifies Ostlehoff's body as being Mulder's. Assistant Director Walter Skinner meets Scully in the hallway, telling her that Section Chief Scott Belvins is requesting she meet with him on the matter. Later, Scully meets with Blevins, Skinner and another Senior Agent. Scully denies that she came to believe in aliens as Mulder does, but admits to her meeting with Kritchgau and what he told her and Mulder. Meanwhile Mulder heads to the Department of Defense Headquarters, getting inside with Ostlehoff's card. Kritchgau intercepts him soon after and tells him that the card gives him higher clearance and potentially the ability to find the cure for Scully's cancer.
The Cigarette Smoking Man heads to Mulder's apartment and is surprised to realize the apartment was being monitored. Scully does some research into the phone numbers that Ostlehoff was calling and finds that they were made to the executive level of the FBI and potentially could have been to Skinner. Scully meets with the climatologist whom she gave the ice core samples to, who says he found a chimera, a new lifeform within them. Scully believes that she can prove the conspiracy if she finds evidence of this organism in her own body and works with him to find whatever evidence she can. She finds Skinner there, who has forensics data on the body in Mulder's apartment and demands she stop lying for him. Mulder meanwhile continues through the Department of Defense Headquarters finding more fake alien bodies inside. He heads through a tunnel to the Pentagon, where he finds an elaborate filing system and warehouse of evidence, ultimately tracking down a small metal vial that he believes may contain Scully's cure.
Scully completes her research, finding evidence that the material from the ice core samples is within her body as well. She meets with an FBI panel led by Blevins that is looking into Mulder's death. Scully explains that Mulder was a victim of an elaborate conspiracy and that she was given a fatal disease by someone in the room. As she's about to present her evidence her nose bleeds and she collapses.
Mulder brings the vial he found to the Lone Gunmen, who tell him its not a cure, but only deionized water.
SEMICOLON-SEPARATED LIST OF ITEMS/LOCATIONS REFERENCED IN EPISODE (BUT NOT LINKED TO IF ALREADY LINKED IN SUMMARY OR GUEST STARS SECTIONS)
- A quote in this episode, "Let the truth be known, though the heavens fall," comes from District Attorney/Judge Jim Garrison, who said this to a reporter while investigating and prosecuting the only criminal case directly linked to the assassination of John F. Kennedy. There are also a few allusions to the Oliver Stone film JFK, such as the extensive use of archival footage in the meeting with Kritschgau, which vaguely mirrors Garrison meeting Mr. X, and the meetings between Cigarette Smoking Man and The Elder at the horse track may be an allusion to Garrison meeting a witness at a horse track in the film.
- The tagline to this episode is "All Lies Lead To The Truth." Symbolic of Mulder's journey of following the path of lies to find Scully's cure.
- For the first time in the series a brief synopsis of previous events is given at the very beginning of the episode, as in "Previously, on the X-Files..."
- The X-Files upgrades to Widescreen 16:9 from this Season.
- The vault that Mulder accesses at the DOD is the same seen in the Pilot and Finale of season 1, where Cigarette Smoking Man stores the implant and the alien fetus.
- Mulder: If this treason should prosper. Mulder says this line in a voice-over narration in the opening scenes from the episode. It is a paraphrase based on the following verse: "Treason doth never prosper: what's the reason? / Why if it prosper, none dare call it treason." It is usually attributed to the Roman poet Ovid. Credit has also been given to English epigrammatist Sir John Harrington. The point of the verse, of course, is that if treason succeeds, it becomes law. Mulder fears that if the people he opposes win, their lies will be accepted as fact.
- **SPOILER ALERT** When the Cigarette-Smoking Man meets with the First Elder in the horse ring, he says, among other things, "I created Mulder!" This is humorous as it is later revealed that he is Mulder's father.
- The ID card with which Mulder gains access to the DOD building is a photo ID, but the DOD guard does not ask to see the ID when he enters. Most high-security buildings would require such a visual identification to prevent exactly this scenario.
- The card Mulder finds in the file cabinet lists Scully's birthdate as 2/23/64.
- This episode features two sections of archive footage from TXF: "Pilot" and another from "Paper Clip". The first clip from the pilot episode shows Scully entering Scott Blevins' office and the second features her, for the first time, seeing Mulder and, simultaneously, entering his basement office. The footage from "Paper Clip" shows Mulder hurriedly finding a file on his sister, Samantha, while accompanied by Scully in the Strughold Mining Company.
- In this episode, Scully says that she and Mulder have known each other for four years. This is incorrect, because their first case together took place in 1992.(even though the show premiered in 1993).
- In Mulder's voice-over he says that his sister went missing 23 years ago. At least 4 years ago, in season 1's 'Conduit', Scully says that she disappeared 21 years ago. The statement here should be the correct one (Nov 1973 - early 1997) making the earlier statement the goof.
- In the white hallway with red doors in the DOD building, there are two doors about ten feet apart, but once through the door and in the room containing the alien bodies, there is no corresponding door to the one Mulder does not go through, but should be about ten feet away.
- Charles Cioffi as Section Chief Scott Blevins
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Bruce Harwood as John Fitzgerald Byers
- John Finn as Michael Kritschgau