Scully, Doggett and Reyes find evidence of a dangerous UFO cult which has found a second spacecraft similar to one Scully studied in Africa two years ago. Misled by the FBI, the agents enlist the help of The Lone Gunmen to protect Scully's son after they learn that the UFO cult apparently intends to kill the child.
On the Canada-United States border, two U.S. Border Patrol agents watch out for illegal crossings. They spot a man on a motorbike attempting to make the crossing and pursue him. After a brief chase, the border guards believe they have the man cornered, but he accidentally drives over a cliff and plummets into a ravine. The bike explodes and the rider is thrown clear. As the rider's satchel lies torn on the ground, papers featuring Navajo/Alien rubbings spill out.
Scully is called into a meeting at the FBI with Kersh, and after entering his office is surprised to see Skinner, Follmer and a few unknown men also in attendance. Despite her initial concern, she agrees to be questioned, and is shown a copy of the alien rubbings from the crash and is asked whether she can identify them. Although she recognises them instantly after encountering identical markings on an alien craft in the Ivory Coast, Scully pensively evades the question, and is instructed by Follmer to cooperate. The men refuse to answer any of Scully's questions, although Kersh admits the rubbings were found in the possession of a man attempting to cross the Canada-US border. Scully claims she wants to cooperate, but is unhappy at not being told the circumstances of the case.
After the meeting, Scully goes down to the X files office and asks Doggett and Reyes whether Follmer has been researching their case files. They deny this, and Scully shows them the Ivory Coast rubbings and explains how she found them. She confirms they are from a UFO, and tells them about her meeting. When Reyes asks what the markings are, Scully describes them as "powerful words", and states that if the FBI is keeping their nature a secret they are aware of their power also.
Doggett travels to the site of the bike crash, and approaches Follmer who is the case's ASAC. Follmer is unhappy to see him, but explains what happened, and also says that the rider hasn't been found. Doggett asks whether anything that "could be found in an X files" has been recovered, and Follmer responds that the case has nothing to with him or the X files.
A short distance away, the bike's rider emerges from undergrowth severely burned from the crash. He reaches into his jacket pocket and clenches an alien artifact which seems to heal his wounds.
Reyes calls Scully to her apartment, where she has been researching the rubbings. She tells Scully she has read that the markings translate into religious creeds, which Scully confirms. She also admits that she had previously refused to accept the possibility that the craft was the source of the world's religions, but now she can find no other explanation for the FBI's secrecy on the matter.
Doggett confronts Skinner outside his office, demanding to know why Skinner has cut off him and Reyes from what should be an X files. Skinner denies the case is an X file, which Doggett is highly critical of. Skinner rebukes Doggett for attending the site without authorization before walking away. When Doggett asks why Skinner is no longer supporting them, Skinner replies that it is because he "knows things" that Doggett doesn't. After Skinner leaves, Doggett breaks into his office and steals the rubbings from the crash along with an FBI Personnel File.
In Alberta Province, Canada, a large weather proof cover is used to protect an excavation, where men seem to be digging up an object. One of the men, who seems to be the leader, scrapes dirt away from a large metallic base which bears the Navajo texts seen on the Ivory Coast craft.
Doggett visits Reyes' apartment, showing her the rubbings he stole and also confirming the identity of the motorcyclist as an FBI Special Agent, Robert Comer, who Reyes knows from a previous case. Doggett explains that Comer has been deep undercover for sixth months. He also admits that he stole the files.
In Jessup, Maryland, Comer attempts to hotwire a cargo truck, but is caught by the driver. Comer, now fully healed of his wounds overpowers the driver and knocks him unconscious, taking his keys and boarding the truck. He searches a road map, looking for Georgetown.
At Scully's apartment, she convinces her mother to babysit William while she goes to speak with Doggett and Reyes. Margaret argues that Scully should not be questioning William's nature, but instead be thanking God for giving her a child and loving him regardless. Scully states firmly that she has to know before leaving.
Scully arrives at Reyes's apartment where Doggett informs her that Comer was undercover in a UFO Cult in Canada, and that the FBI is covering up his identity because they believe he was converted by the cult. Doggett also tells her that Comer is now missing. Reyes reveals that Comer's rubbings do not match those from the Ivory Coast, suggesting that they are from a second Alien craft.
Margaret returns to Scully's apartment with William after a walk, and is confronted inside by Comer, who overpowers her and shuts himself in William's room with the baby. Scully arrives and finds the door open, discovering her mother who says a man is trying to kill William. Scully enters William's room with her gun ready, but is ambushed by Comer who is able to throw her out of the room and disarm her before locking the door. As Comer prepares to smother William, Scully breaks through the door and guns down Comer with her back up side arm.
Doggett and Reyes rush in to find Margaret injured, and are met with Scully who asks Reyes to take William and her mother somewhere safe. She complies, and Scully leads Doggett through to where Comer lies dying from gunshots to the stomach. A highly shocked Doggett exclaims that Comer has to be taken to a hospital, but Scully insists that she has to find out the truth from him before they allow the FBI to clean up their own mess. She angrily demands to know why Comer was trying to kill William, and Comer weakly replies that her son "has to die". A hysterical Scully screams at Comer, asking why. Doggett calls an ambulance.
Comer is taken away by paramedics in serious condition, and Scully confirms that Comer intended to kill her son with a pillow. After Doggett has left, Scully notices Comer's jacket and searches it, finding the Alien artifact.
In Calgary, Canada, one of the cultists, a woman wearing an overcoat, sees a newspaper headline reporting Comer's shooting, exposing him as an FBI Agent. She rushes to the site of the dig and informs Josepho, who says that it "changes everything", before confirming that there is only "one thing to do". The woman shows her understanding and leaves.
At the J. Edgar Hoover building, Scully and Doggett are called into a meeting with senior staff identical to that faced by Scully. She immediately shows her scorn towards her superiors, describing the meeting as a "secret interrogation", while Doggett agrees, citing the FBI's "hush hush" as a cause for suspicion. Kersch admits that Comer was an FBI Agent who had infiltrated a UFO Cult led by a former US Military Office. He goes to explain that Comer was given the assignment due to a series of threats on Mulder's life. When Scully asks why she was not told this, Follmer admits that Comer had received reports that Mulder was dead.
Reyes brings William back to Scully's apartment, and Reyes quickly realizes that something is amiss. She questions Scully, who begins to tell her about Mulder when the drawer housing the Alien artifact begins to shake violently. Reluctantly, Scully opens the drawer, and the artifact flies out and hovers over William's head. William serenely stares up at the object as it levitates over him. Called by Reyes, Doggett rushes to the scene and meets her. Reyes explains what happened, much to Doggett's startlement. Scully takes William into her car to take him somewhere safe, and Doggett notices Overcoat Woman watching them from in her car. As Scully and Reyes drive away, Doggett confronts the woman at gunpoint, but she runs him over and knocks him unconscious.
Scully drives into an abandoned alleyway, where they meet the three The Lone Gunmen, who agree to look after William while Scully attempts to find out who is pursuing him. Scully says an emotional farewell to William before leaving with Reyes.
They return to Scully's apartment, finding police and ambulance teams. Skinner informs them that Doggett is in a coma after having been run down by an unidentified woman. Realizing the danger, Scully returns to her car and drives away.
As the Lone Gunmen meanwhile head to a safe location, they are ambushed by a woman who opens fire on their van and knocks the vehicle off the road. With Frohike and Langly incapacitated, the woman opens the back door of the van to find Byers holding William inside the vehicle. The woman puts a gun to Byers' head, threateningly.
Cast and Characters
- Alan Dale (Toothpick Man) previously played Michael Wilhelm in The Lone Gunmen (TV series) episode "Eine Kleine Frohike".
When the show cut to the scene to Calgary, Alberta, Canada, they got somethings right, like the Calgary Tower, but when the showed the foreground scenes they got it all wrong, making it look like a standard US city and Calgary does not have any news stands that they had shown.
- Gillian Anderson as Special Agent Dana Scully
- Robert Patrick as Special Agent John Doggett
- Annabeth Gish as Special Agent Monica Reyes
- Mitch Pileggi as Assistant Director Walter Skinner
- Cary Elwes as Assistant Director Brad Follmer
- Bruce Harwood as John Fitzgerald Byers
- Tom Braidwood as Melvin Frohike
- Dean Haglund as Richard Langly
- Sheila Larken as Margaret Scully
- Neal McDonough as Agent Robert Comer
- Denis Forest as Lt. Colonel Zeke Josepho
- James Parks as Agent Terry Sullivan
- McNally Sagal as Overcoat Woman
- Alan Dale as Toothpick Man (First appearance)
- Joe Colligan as Driver Agent
- Brian Catalano as Agent Daley
- Randy Hall as U-Haul Driver
- James Riker and Travis Riker as William Scully III
- Laura Leigh Hughes as Kersh's Assistant